Don't think that your issue is related to PrPro version. I'm still on CS5.5 and never had an issue with image sequences.
Regard to frame rate, as I said, if you deliberately shoot in 24 fps (which is likely 23.976 and, therefore, NTSC), be stick to it and edit and export in 23.976 fps. Since your goal is to upload your video on YouTube and not to deliver it to a Norway or any other European broadcaster, don't bother about PAL too much.
However, as I also mentioned, I don't think that your ongoing issue is caused by mixing frame rates - I have no problems with interpreting numbered stills as 23.976 fps, editing in 23.976 fps and exporting as 24p. Something is wrong with either your footages or your system. You'd rather upload your test project along with some of your problematic stills with which you can reproduce the issue (either old good flickering or the new one with a nice completely black screen) so that we could test them on our machines.