Problems with Render Effects In to Out

I posed a couple questions in my last thread, but only one was answered, so I'll post my main question in its own thread. Often, when I create previews for a sequence with "Render Effects In to Out," some aspect of the sequence is changed. A couple times, when I had multiple clips playing in the same window, the frame sizes of a couple of the clips changed after rendering. The past time I did it, one of the clips started to look like it was playing in slow motion even though the speed/duration setting claimed to be at 100%. In both of these instances, the affected clips looked the way I wanted before rendering. Any idea why this is happening? This is with Premiere Pro CC, if that helps.
Thanks,
Cody

I'm trying to pull something together to show you, but of course, the frame size change isn't happening. The frame rate change (that's what I think it is, anyway) is happening though, but it's strange. I have a clip in one project, and before I rendered this clip, the preview looked fine, but after I rendered it, it looked like the frame rate had changed. I tried exporting, and that looked off too. I tried removing the clip, placing it back into the sequence and exporting without rendering, and it looked off. It seems like there's something going on with this project file. I opened a new project and put this same clip into it and the clip rendered and exported just fine. I didn't put any effects on this clip in the either project. I don't know if there's a way to add effects to a video track, but if that's even possible, I don't think I did that either. I can upload a small clip of what it's supposed to look like and what it looks like when I export from the first project if you think that'll help.

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Model Identifier: MacPro6,1
Processor Name: 6-Core Intel Xeon E5
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Memory: 32 GB
Boot ROM Version: MP61.0116.B07
SMC Version (system): 2.20f18
Illumination Version: 1.4a6
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