I've just upgraded to 2.5.28. This didn't happen with 2.5.21. mldonkey simply doesn't commit finished downloads. In kmldonkey, i can see them in the "commit" list, but they're never processed, even if I manually press "commit" on them. User p2p _does_ have write permissions for /home/p2p/.mldonkey/incoming, and I've got plenty of free hard disk space on /home.
I've downgraded to 2.5.21 and all downloads that were stuck in the commit queue were committed. I'd suggest to mask out 2.5.28. I haven't tested 2.5.27.
:/ I didn't notice that it was already masked and I had it in package.unmask. :P However, 2.5.21-r2 is stable and I can't see the reason for masking it.
2-5-21 is unstable compared to 2-5-28, but 2-5-28-r1 has a new behaviour in regard of handling the incoming directory. See this patch: http://savannah.nongnu.org/patch/?func=detailitem&item_id=3297 and this thread http://mldonkey.berlios.de/modules.php?name=Forums&file=viewtopic&p=14681 for further explanations.
not a bug, but a feature, then. sorry for the great delay.