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It is possible that your app is broken (using free twice on a zone or something like that) and there's different behaviour between AmigaOS calls and gcc calls.
Have you used memminister to ensure that all memory is freed on exit? Maybe some free() fails in the way and corrupts the memlist.
I've worked a lot with gcc (on Linux/Windows). When you're lucky, it crashes in the free() call. When you're not lucky it crashes in the next malloc()!!
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