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It is common practice then temporary breakpoint used to stop on main(). Normally, it is installed by 'tbreak main' GDB command as scripted in startup session routine. During debug session it usually hit and removed from GDB, but not from Breakpoint View. So, on next session start Eclipse tries to restore this breakpoint, while GDB script tries to install it as well. As a result there are two breakpoints in GDB, and it is confusing. My point, removing all temporary breakpoints upon session termination may helps.
A case how to reproduce this bug: 1. Create a C/C++ project with main() and foo() functions. 2. Build. Open debug configurations-> startup tab- see "set breakpoint at: main" 3. Debug. terminate 4. From Debug configurations set a BP to foo() function, debug again. 5. Open Breakpoint View and check Observed behavior: Has two temporary bp in breakpoint view Expected behavior: Temporary breakpoint at step 2 ("main") is removed