I have been playing HBD for awhile now and had never had any problem with pitcher
fatigue in the ML before but suddenly now two of my teams are experincing crippling
pitcher fatigue on the ML level,even when I drop their pitch counts below where I usually
have them for their stamina,..has anybody else had this problem recently and are there suggestions
on how to deal with this problem?

Did you have a string of extra-inning games within a short period of time, with no off days?  That can easily do it.

It could be the make up of your staff.  Maybe you just don't have enough DUR/STA for your SP's and bullpen.

Lowering pitch counts might not help much because the pitches you're cutting from one pitcher are just going to go to another.  Fatigue may still show up, just on somebody else.

You need to stay on top of pitching fatigue on a game by game basis.  What I do occasionally, when I see fatigue starting to creep up but before it becomes a problem, will be to "sacrifice" one of my starting pitchers by jacking up his TPC/MPC to the max, with a call bullpenrating of 1.  Basically, trying to force a complete game out of him to save the bullpen for a day.  Or (better yet) tandem him with another SP or LR type to save the bullpen for a day.

If it turns out to be a chronic, recurring issue, maybe you just need to drop a position player from your 25 and add another pitcher.