If I understand you correctly, you have two different threads (the main perl interpreter, and a C++ thread activated by an interrupt) both accessing the same perl interpreter. This is a big no-no, and corruption is going to ensue.
The basic model of perl's current threading implementation, ithreads, is that each OS-level thread is given a separate perl interpreter, so that if they run in parallel, they can't stomp on each other's data. The perl internals just aren't designed for concurrent access - there are no internal locks protecting each SV and/or critical code sections.
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