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1) if I understand you correctly, you're copying and pasting clips. Clips are independent entities once created and changing one contents doesn't affect any of the others, unless they refer to same file. Are you saying that some copied clips don't play at all?

2) the tools menu is only available per MIDI clip; however, you have the normalize and quantize commands under the Edit/Clip menu-- just make a track region selection, and left-click to invoke this Clip context sub-menu. Take care that Normalize applies to both audio and MIDI clips while Quantize only makes sense on MIDI ones.

3) when you don't have an instrument definition setup, bank/program patch numbers are zero-based (0-127); however, in MIDI track dialog the drop-down list will show and let you select program numbers in 1-base fashion (1-128)--yes, it can sometimes seem strange and misleading--I'll see ;)

HTH
Cheers