When adding a tool to the tools menu, it adds 2 "Configure Tools" commands, one above and one below my added tool.
Doing a series of add tool, remove tool gave me this (very weird :)) menu:
Configure Tools
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Visual C++ Compiler
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Configure Tools
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A
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Configure Tools
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A
B
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Configure Tools
When CodeBlocks is closed (or crashed :)) and reopened, the Tools menu becomes correct. So this problem doesn't persist across sessions.
Yes, it's a known bug :(
I plan to fix it soon.