Are the rotating gears video clips? Or animated images from Phtooshop (or wherever)?
My guess is that they're images and that you have the opacity level turned down in the PSD (or other format) files themselves.
If that's the case I can send you some very simple steps to fix them in Photoshop.
Also, if they 'fade in' then they're supposed to be semi-transparent (from 0-99%) until that fade effect ends. So, if you're looking a that part of the clip, you're seeing what is expected. But there are some ways toy work arounnd that as well.
In either caseI need to know the speciics before I can send you steps to 'fix' it. Screenshots help. A lot.
They are .psd images that I took the outline of our gear logo and filled in with another image of steel. So it makes sence that the psd file has lower than 100%. How do I fix that? convert to jpeg?
1. In the project panel, right click on the image(s) and choose 'Edit in Adobe Photoshop'
2. In photoshop, with that image open, go to Layers pallette>transparency and make sure it is set to 100%. Also, check the blend mode to make sure it's set to 'normal'
3. Save the image in PS and return to Pro and it should be fixed
NOTE: If the psd has many layers you may have to do it for each layer
And if that doesn't work, now that I mentioned blend modes, check the blend mode for the image clip in prPro (it's in the effect controls under the opacity twirl down). I don't know how you could have gottent that set to anything to normmal without knowing it, but it's a possibility.
Especially if the "gears" are on a Transparent Background, i.e. knocked out, you do NOT want JPEG, as it does not support Transparency, and it also will compress the Image. Keep the PSD format.
I think that Jstrawn has given you the things to check, otherwise.