Well as I said, Geany does NOT store anything about running subprocess state, and even if it did nothing gets stored if its crashed. Thats why I am suspecting that your laptop is suspending or hibernating when its battery goes flat, which may store Geany's in memory process state and restore it hence getting the same menu state. I note that suspending works as advertised in your experiment, if you still have battery, but maybe its not so reliable if the battery dies. But Geany has no knowledge of suspension and resumption, so its nothing it caters for, its entirely up to your OS and desktop if it works and Hiesenbugs are common in Linux suspend/hibernate/resume IIUC.

The menu behaviour is as it was intended since 0.19 (IIRC) but its possible that in the past there was a bug in the process spawning code that returned the menu immediately, but the spawning code was mostly re-written at some point since then, possibly removing the "unintended feature". This change in behaviour has been pointed out before, but AFAIK no conclusion was reached as to why it happened, but as I said its now working as intended. Did you try running the terminal from a shell and detaching it to allow multiple terminals?

Your environment problem is most likely because you do not start Geany from a shell (maybe a menu or shortcut). In that case nothing reads your shell startup files to set PYTHONPATH so Geany does not inherit it. Changing the menu/shortcut command to run Geany from a shell should fix that. Tell your distro packagers to fix the menu/shortcut, Geany does not make that. Alternatively your distro may have aliased sh to dash not bash so again the startup file is not read.

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