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Could you potentially post your project to the web, or one that has a similar problem, and share the link? I understand the general problem, but it's difficult to get your particulars.
The cream colored transitions are "helper" transitions that exist to get everything to work smoothly. Catalyst 1.0 creates these because it needs to add some extra transitions under the hood to make everything work visually the way you'd expect. For every "reset" you're hoping to take effect, you should have at least one green bar.
One last thing to check out, is that components resize a little unpredictably in Catalyst. There's a little bit of a discussion of that here.
Thank you for the explanation of the "helpers", that information has lead me to discover the overly simple explanation to why things weren't working the way i had set everything up.
Basically the issue was that the Custom Components that i had built for each main state were still in their originating folders in my layers pane. i set them up as Products, Videos, Our Team, , Contact, and Partners. It was this finding that i figured out that if a custom component is left in a folder the timeline recognizes both the component and the main state layer. I only had transitions/actions applied to the component itself and none applied to the video layer (the video folder in the layers pane), partner layer, contact layer, etc etc. . So Catalyst only saw the "no transition" on the those layers and caused them override the actual component action.
I don't know why i hadn't noticed it before, i'm definitely still learning but it explains why the product component continued to work just fine and thats because it wasn't in a folder in my layers pane like the rest were. once they were removed from the folders and the empty layers/folders were deleted. Viola! problem was solved.
Thank you so much for the insight, and hope this helps anyone else that runs into a similar problem.