Trouble replacing clips with comps

[michaelr12718676]

There are a few clips in my timeline that are sped up (150%). I sent these clips to VFX, and when I go and replace the footage with the comps, most frames match with proper TC, however there are some that aren't matching. I can work around this by splicing those individual frames and returning the speed down to 100%, however I'd prefer not to do this. 

Furthermore, there is a scale in and I noticed that as the clip is animating, the frames do not match even though the velocity, position points, and scale are all matching. How do I fix this?

Thanks

[Richard van den Boogaard]

Working with speed adjustments along with other parameters will not give the expected result.

Please try the following: adjust speed and then nest the sequence. Next, apply other effects to the nested sequence.

[Mike Dziennik]

Are the speed adjustments baked-in from VFX? And how are you replacing the clips? Alt dragging from project panel?