I have recently (eg 6a0852b8e5a8) noticed the following behaviour, although it may be older:

I start

isabelle jedit Analysis.thy

let it run for a little bit, then double-click on some of the early theories in the Theories panel (probably one it has processed already or is in the process of doing so) and after a little bit double-click on theory Analysis in the theory panel, this double click is usually ignored. Often a second double-click is ignored as well. Typically the fan is quite busy. Eventually (12-20 secs?) a third double-click returns me to Analysis.thy.


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