The problem could be that the IDB is fragmented, and it is taking a very long time to collect information from the IDB. If I suspect that the IDB is fragmented, I have folks run
omnidbutil -info
and check the 'catalog' part of the output, specifically, at the ratio of REcords Used vs Records Total. We like for this to be as close to 100% as possible, certainly over 90%. If the ratio is lower than that, we recommend a purge of the IDB
Also, Backups are probably stressing the CPU, especially if you are backing up a large number of small files, and may cause everything to slow down