Clearly this is a problem with your card since it isn't effecting your friends M3.
YSMenu might solve the issue... it might not, but it's worth a shot.
Another source of the problem could be your MicroSD card.
I'm experiencing the exact same lag on pokemon, both, pearl and diamond. And i've narrowed it down to the problem is the MicroSD card.
I got a 8Gb card Class 4 MicroSD SDHC from Silicon Power, when copying to and from the card it performs like a class 4 card.
However Pokemon Pearl and Diamond lags to the point where it is unplayable, everything it slow, music plays in slowmotion, you walk slower, the bag is a hell.
The exact same game works like a charm on the old Fire Card DS i had bought my son.
So i tried formatting it everywhich way, 64Kb, 32Kb using dos and SDFormatter. no luck slow no matter how i did it.
Then i found an old 512Mb MicroSD card from my old phone (Nokia N95), and tried installing DSTT on that and Pokemon Pearl and Diamond, and vupti it runs fine, no lag at all.
So my guess is there is some problems using SDHC cards with DSTT.
I've tried the laggy card on 2 diff NDS machines with the same result.
So for now the kids are stuck with their Fire Card DS instead, while i try to contact the place i bought the DSTT to see if this is a known problem.
I might as well add, i've tried with the latest firmware, even the japanese one with updated libs and all but to no avail.
Dont have any more MicroSD cards to test with
But kinda guessing the standard nokia microsd card would be slower performing than the new 8Gb, hence leaning more toward the problem being with SDHC... could try formatting the card with 4kb limiting it to 2Gb to see if that changes anything