I have often problems with the wallet (hobonickelsd, running on Ubuntu Server 14.04, compiled from latest git source).
It is often stuck on something like this (snip from debug.log):
05/07/14 10:13:40 ProcessSyncCheckpoint: pending for sync-checkpoint 0000000002bde252b09a26e27d6c96d5594ca6340d6ff2de5138ca8a1f90d715
and it takes 100% CPU for a very long time or almost indefinitely without doing anything apparently useful.
When I restart it, it can run for few hours or even days fine before this happens again.
Any idea?
is this a fresh setup, meaning are you downloading the blockchain from scratch?
if so, it might take a while and to catch up and those are normal check IMO.
you could try to download a "bootsrapped" version of the blockchain and start from there.
try this http://wiki.hobonickels.info/index.php?title=Replace_Blockchain