I got the same problem, random freezing when im playing diamond or pearl. I've only just got my R4+1GB jap kingston, shouldve gone with the M3 simply :/ .
I've noticed a tiny, tiny bit of slowdown when going through the battle menus sometimes, but that's definitely negligible.
Oh, and I'm using a 1GB Japan Kingston with my R4.
exact same thing happens to me aswell, and the game has also frozen when in the pokedex, i touched the area tab when viewing a pokemon and the game just froze with a black screen with the tabs still showing, music playing in a loop, the first time my game froze is when i left the game for about 45 minutes to check my email so i put it in sleep mode and was charging the DS lite i came back to resume the game, opened the DS lite and the game was just frozen, i was real mad then because i didn't save for quite a few hours
anyway Ive tried formatting to FAT and FAT32, got no other stuff on the card, and went back to kernal 1.07 and still freezes..
also i have noticed recently that when i change something on my R4DS after putting it into my memory card reader and putting the micro SD into the R4DS and then into the DS lite and turn it on, the R4DS is not recognised, it just shows the health and safety screen and when i touch it and go to the main DS menu there is nothing shown on the DS part, just empty, when i turn off the DS lite and blow into the slot and turn it on again it goes back to normal, this problem has been increasing more and more now, before it would happen rarely, but now it's happening almost every time i upload new stuff to the micro SD.
exact same thing happens to me aswell, and the game has also frozen when in the pokedex, i touched the area tab when viewing a pokemon and the game just froze with a black screen with the tabs still showing, music playing in a loop, the first time my game froze is when i left the game for about 45 minutes to check my email so i put it in sleep mode and was charging the DS lite i came back to resume the game, opened the DS lite and the game was just frozen, i was real mad then because i didn't save for quite a few hours
hrm. That's odd.
I've yet to have any freezes from sleep mode, and I've left it in sleep mode over-night while charging on numerous occasions.
Hell. I've flipped my DS in and out of sleep mode a good 10+ times within the past hour to play Pokemon on and off, without saving and all without fail.
It is possible that it's the card itself, considering there are manufacturing defects and the like, however small and insignificant they can be sometimes.
Or, it could be a random defect in the R4 itself, too.
But iunno. I've only had an R4 for the past month(same goes for my DS), but so far the only freezing I've had was with the Pokedex like I mentioned before. And I doubt it's only from a small amount of playing, considering I've got over 30 hours logged in on Diamond, and have played through a few other games before Pokemon even came out.
Oh, and I've got my MicroSD formated to Fat, as opposed to Fat32.