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You are correct with the order of events. The problem was persistent across multiple restarts and even multiple reboots. Interestingly enough, when I came in this morning, the correct paths were there. My PC was rebooted overnight for some software updates (not SecureCRT related). I'm at a loss on this one, but it appears to be working correctly, at least for now.
I'm a long time user of this software and this is the first issue I've had with it, I've been otherwise extremely pleased with it and recommend it to anyone asking for a terminal emulator or SSH client.
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