I was using the 6.x-2.2 version of Poormanscron on my site, and had it configured to run every 24hours, but each time it ran, my site was left "themeless", whereby my default theme (customized BlueCurve theme) was enabled, but the Default option was unchecked, thus contents were not appearing correctly and after mush investigation came to the conclusion that it was Poormanscron execution which resulted to this.
I had to disable Poormanscron for my site to be back to normal again, and so far no problem, even when I run cron manually.

Anyone can investigate on this, and/or provide me an alternative to solve this issue?