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aha. you're doing it all from the main tracks view (main menu Clip > Tools > Rescale...). i was trying instead on individual clips to their MIDI clip editor alone (menu Tools > Rescale...).

and yes, i can confirm that on the second clip, the one that first note isnn't at beginning of the clip, gets it somewhat mistaken on the anchor time reference. let me tell this is not a bug in it's own sense, in fact, it's all working as signed: although, on the main view you actually see a course selection, which spans over the a clip region, for the MID tools it actually means about the events are selected directly as it would happen on each MIDI clip editor on it's own, so that on each clip, the earliest event that get's inside the selection range, is indeed the anchor reference for Time rescaling... the issue you're observing is that this starting event most probably isn't on the very same on-set time and so, time rescaling might get skewed across several tracks.

the other issue, that goes for the copy/paste, is still under investigation, but the thing you shall be acquainted is about when copy-pasting whole MIDI clips, the copies are said linked or, in other words, they represent the very same MIDi file track/channel contents. You can unlink those copies via, you guess, menu Clip > Unlink. With v0.7.9+ you can also get some visual evidence that two or more clips are linked: you click on one and the linked others are shown with a dashed light-blue outline.

and yes, just confirmed the loss of undo. investigation's still an on going process... thanks for all the details.

byee