Third party transitions incorrectly scaling footage

I am working on a PSA that is largely made up of still images. I am experiencing issues with multiple third party plugins (Boris and Coremelt, mostly) when setting up transitions. Here is the problem:
Track 2 has an image that fills the frame. Track 1 has an image that does not fill the whole frame (pillarboxed). I want to set up a transition from V2 to V1, but during the transition, the image on V1 is stretched to fill the frame. After the transition, the image is fine.
I seem to have fixed it in certain circumstances by nesting the image, then selecting that video track as the incoming track. (In one instance, the nest on V2 was read by the plugin as being V5, and if I tried to change the selection to V2, it kept V5 selected. If I selected V1, it switched to V4. What?)
It also occurred with a video clip on V1. The video filled the frame, but during the transition, the video was scaled up. After the transition, it was back to 100%.
It only seems to be a problem with plugins in which I need to select the track to transition to. The plugins that only affect the top track don't seem to be a problem.
Has anyone experience a problem like this before? Any advice?

I can't talk to coremelt, but I use Boris.  Boris will determine what the sequence format is and will use that for all clips in the sequence. For a transition to work, the incoming and outgoing clip have to have the same format. That's why what you identify as incorrect scaling is occurring and only affects the images during the duration of the transition.  When you apply a 2 second transition, the program takes 1 second from the outgoing clip and 1 second from the incoming clip and creates a new clip 2 seconds long to fill the gap.  That's why the issue only shows during the transition.
If I understand what you are trying to accomplish overall, you are making this far to complicated.  For Boris, the still image used as a PIP doesn't have to be on a Premiere track.  You place the Boris effect on the background clip in premiere.  Open the Boris effect controls.You create a media plane above the background.  click on the image icon for that plane and browse to the image you want to use as a pip and click.  That image should now show above the background in its original size.  Use the transforms for the pip media plane to size and position the pip and apply borders or shadows as you see fit.  keyframe the opacity on the pip media plane to fade in and fade out the pip as you need.  If the pip image resolution and pixel ratio differ from the background, you can change the values in the pip image track properties.
If you don't want to effect the whole duration of the background clip, place transparent video clips of the desired length on the preniere track above the background track and apply the effect to the transparent clip.

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