Yes, PNG graphics can slow the response down, particularly if you have PNG buttons on top of a PNG background. It's incredibly graphically intense for the processor of the 3000.
So, working towards narrowing down your specific issue:
If you've got really slow hard buttons, are there sounds programmed into the button presses? Long sounds can slow down a button reaction. Other than that, are the IR codes learned or are they from the database? Codes that have been learned with errors can sometimes cause slow button presses.
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