I have the exact same problem. Game runs fine 50-60fps and after few minutes, regardless if I'm running around or standing still it starts spiking every 2 seconds. Tried reinstaling multiple times patching with mcpatcher and optifine to no avail. Though after the first time I've copied OptiFine_1.2.5_HD_MT_AA_A7 files to minecraft.jar I had no problems for like 3 days.
By the way,
- freeing up C drive space didn't help.
- changing texture packs (16x 32x 64x) does not make a difference.
- adding java.exe to nVidia 3D settings list and setting java to Full Performance dind't help.
- fresh install no difference.
- in my case, fps was more likely to start spiking after i jetpacked down my massive quarry witch then results in series of fps spikes.
I don't think it's a hardware problem, for me vanilia minecraft with 128x texture pack, far render distance, 90 FOV and fancy settings is running about 100-150 fps.
I've run out of ideas.