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Often when I switch to the free select tool, I find it has switched itself into intersect mode. This appears to also be the case for the rectangle select tool. This may be more of a general problem with tool options automatically changing over to the right most position, as the move tool is switching into path mode on it's own too. I've tried setting them to the left most option, going into edit>preferences and saving the tool options. It didn't help. What could I be doing that would change the options on multiple tools that aren't selected?
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Gimp on its own does not decide anything. Up to the user to make those decisions.
What it does do, by default, is remember the last used settings and each tool keeps its own settings.
Rectangular select in replace mode and if sometime in the past you set free-select in intersect mode or move in paths mode.
If you change back to replace mode for each, then these save when Gimp is closed.
If that does not happen then maybe something stuck in your Gimp user profile.
try: Edit -> Preferences -> Tool Options then Reset Saved Tool Options to Default Values
It is possible to set Gimp up so that the tool settings are fixed when Gimp first starts. There is a on/off toggle in Tool Options "Save tool options on exit"
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You might Ctrl+Shift while using a filter and the select tool is active or Ctrl+Shift to soon before switching tool or some fast habit with Ctrl+Shift
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I've experimented with CTRL-SHIFT with the tools selected - if the normal mode is selected, all combinations of ctrl and shift are temporary. The tool returns to normal when they are released.
In the behavior I am observing, the select tools permanently switch to intersect mode. Until I select normal mode - but they soon return to intersect mode.
I wonder if num lock is causing this? I just noticed that it's been on this whole time. I've turned it off, will see what happens.
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O.K., I finally caught it in the act - it's the shell script remapping my Cintiq buttons that's doing it. It worked fine under Kubuntu but there's a problem in OpenSuse. Maybe I can solve the problem by configuring the Cintiq in System Settings instead of using the shell script.
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Still not there - I got rid of the shell script but shift and ctrl still cause problems when used from the Cintiq buttons.