When capslock is on, the currently selected region is
merged with each newly selected region. When caplock is
off, the newly selected region replaces the previous
one. All is well and good.
Sometimes, jEdit gets confused and applys the merging
behavior when capslock is off and the replacement
behavior when capsloc is on. This is a per-text-area
bug, as I often end up with multiple panes where some
of them have one behavior, and others have the other.
Turning capsloc on/off while other apps have focus
doesn't seem to affect it.
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Java only notified apps when caps lock is pressed, but not
if it is currently active or not. So yes, the selection
state can get out of sync. However, it is maintained on a
global basis (all text areas share the same setting) so it
cannot fall out of sync between different text areas (unless
you have multiple instances of jEdit running).
If you don't like this, change the keyboard shortcut of
'Multiple Selection' to something else.