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I've noticed a similar problem with my two-way player (SP/C), so I decided to try a Starting Pitcher to compare perk progress, and here's what I've noticed:

The description for hitting perks says "... drive in runs, move the runner over, and rack up clutch hits...", which seems to be pretty straightforward. I have the difficulty cranked way down, so these happen a lot.

The description for pitching perks says "...strike out batters, hit your spots, and keep the scoreboard clean..." With the difficulty set very low, I 'seem' to do this a lot with my two-way player, but perks aren't unlocking. With my SP, however, I started to notice "high leverage outs/strikeouts", and have unlocked a few perks shortly after getting a few of these. The "high leverage" situations I've seen so far are:
7th inning, game tied at zero, runner on base, final out
8th inning, game tied at zero, bases empty, first out
9th inning, game tied at zero, bases empty, first and last out
extra innings, game tied at zero, runner on second, first and last out

With my SP, these occasionally happen because the offense gives me no run support, but with my two-way player, they never happen - because we are never tied (or losing) in the 7th inning or later when I am both pitching and in the batting order.

The Fielding perk description says "... highlight-reel catches and flawless plays...", but my SP unlocked one during a routine groundout where he wasn't involved in the play, and another striking out the batter for the second out in the third inning, so I don't know what's going on there.

I haven't really tested out the Baserunning perks, so I have no insight to offer for that.

I hope an upcoming patch will improve this.

@randy.sorensen_MLBTS

I decided to download update 7 and see if the same magic would happen for me, and it did - I unlocked 2 pitching perks.

It was my SP/C's 7th start in the majors (at the end of May, so still before the All-Star break - which was mentioned in a previous post as a point where some had gained a perk). After striking out the first batter in the 4th inning of what was at the time a 1-0 game (we were winning), I unlocked the First Strike perk. At the end of the game (a perfect game - I did mention I have the difficulty set really low...), I also gained Pulse Pounder.

There were no 'high leverage' outs in the game, but there was a successful boss challenge and a couple of successful dynamic challenges (pitching related - no challenges came up when I was at bat).

I checked the patch notes, and as you noticed there was no mention of anything regarding perks in the RTTS changes.

Which means I am now back to not understanding what is going on for unloicking pitching perks. No direct correlation that I noticed for anything that I suspected would trigger it.

Hopefully that means something has changed for the better, and I will go back to playing as my two-way player.

I will post any further observations in this thread (unless it gets locked) if I learn anything useful.

But for now, I have to decide if I should spend the tokens I just earned on improving my stats or upgrading Pulse Pounder...

Here is my most recent update/findings.

My SP/C character (who did not go to college) is now at 40 career pitching starts at the MLB level, and has unlocked all 23 hitting perks, 11 of the 14 pitching perks, 10 of 11 fielding perks, and 5 of 9 baserunning perks.
I still get offered the 'bugged' dynamic hitting challenge with a perk reward while batting (the one that is impossible to complete) - even though I've already got all the hitting perks.
I haven't unlocked a new pitching perk in over 10 starts, which is seems odd to me - they've all been complete game shutouts (or better - I did mention I'm playing on low difficulty).
For baserunning, I only recently started to improve those stats, and my habit had been to skip most baserunning opportunities, but I now have 37 carreer SB, which is probably why I've started unlocking those perks.

One other thing that concerns me... In one pitching start, I got the notification that I was injured, which I decided not to accept, so I hit the 'simulate and exit' choice (I had autosave turned off) to quit the game. In the post game progress screen, it indicated I had unlocked a pitching perk (Last Stand, I thnk), but since the injury result had me sidelined for 2-3 months, I decided to exit and reload my save. That was over 10 starts ago, and no additional pitching perks have unlocked.

I switched back to my SP-only character (who did go to college - so a headstart on unlocking pitching perks) for a comparison, and am now at 25 carreer starts in MLB, and has unlocked 12 of the 14 pitching perks, and 5 of the 11 fielding perks. My most recent pitching perk unlock happened in start 19, and I can't remember how long it's been since I unlocked a fielding perk.

I finally did experience a potential perk reward in-game challenge as an SP, but it was a Boss challenge, not a dynamic one. I once again found myself pitching into extra innings (zero run support from the offence), and in the 11th with the score still tied at zero the opponent's cleanup hitter came up, and I got the Boss challenge. Only one of the 3 potential rewards indicated a perk, but it looked the same as the 'bugged' hitting challenge - color indicated an unnamed hitting perk, and even though I seemed to achieve the task (strike batter out on 3 pitches), the challenge did not complete, and only 'failed' when I got removed for a relief pitcher after the 13th inning. It seems that one is 'bugged', too.

I also find it odd that the only way for a SP-only character to improve one's Speed attribute (which would still be needed to cover 1st base on ground balls) is through off-day training sessions - which means 1 point at a time. There's no way to spend tokens to do that.

I see that patch 8 has been released this morning, and the patch notes once again don't mention anything about fixing perk-related problems in RTTS.

I guess more testing is needed.

This 'bugged' hitting challenge (with the potential perk reward) seems to still be 'bugged' after today's patch/update 9.

This hasn't happened to me yet, but I've seen it mentioned by a few others on this forum - no one has ever mentioned how to fix the issue.
If this is going to continue to be a problem, then I'm going to have to treat RTTS like other RPGs and use multiple save files (alternating between them) so that I don't lose too much progress when things go bad.
Which would mean that we need to get SDS to increase the save file limit.
I like to have a couple of different types of RTTS careers going, and a hard limit of 10 files isn't really enough if I have to start keeping backups.