I posted about this over at emule-project.com and it was moves into the 'offtopic' section...
Anyways, it's all because of the new server software that don't want people downloading many files at once. A 'work-around-fix' was apparently implented into the .30 series of emule in order to fix it, but not very successfully.
I've switched to overnet and am enjoying amazing speeds constantly now. Downside is that there aren't sources for the rare files, and that I have to convert all the part files when I switch back to emule again.
I'm currently waiting for the 'emule 0.29c Xtreme 1.2' mod (a continuation of Maella's work) to get updated into a .30 version. Hopefully that'll give good speeds again.