I've been having a version of this same trouble lately with my Type IXB. Not sure when this bug appeared, as I do not remember having this problem in my first career (the only other one I've actually had a Type IX in), but then again that was many months ago and I lost my Type IXB on my first patrol with it (an Operation Drumbeat patrol to the US coast) and I'm not sure I got off enough shots to even need to reload from the stern externals.
I'm running GW now, and I have to put a bunch of people into my bow compartment before it will let me bring the stern externals aboard the boat. Once I do that it at least lets me go ahead and bring them aboard though - I haven't had it give me a time and then not count it down or eventually bring them on board, so I'm not sure what that part of the problem might be.
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