The different toolbar buttons behave between skins against Adobe programs could be based on the way the skinner makes its skin, some programs (the more modern ones) use Windows Vista/Windows 7 guidelines for its controls, so the newer model have toolbar buttons with 6 states instead of 5, used in the older XP Explorer.
The 5 and 6 frames model also have different states order:
• 6 frames (new) model: Normal, Hover, Pressed, Disabled, Activated, Activated-hover
• 5 frames (old) model: Normal, Pressed, Disabled, Hover, Default
Conclusion: some skins that does not have all toolbar buttons section skinned (view in SkinStudio) could be using the old buttons model in more modern programs that need the new model, missing and alternated frames order could be the cause of your issue.