First, I'd like to apologize for posting on the old thread - I'm not sure how I landed there, actually. But here I am now, on the correct thread (the wrong thread again, why??), and... I can't get the error to reproduce in "stock," which I assume in this case means no mods other than Scrapyard and its dependencies installed (MagiCore and Module Manager). I do NOT have Kerbal Construction Time installed, as every search for an up-to-date download seems to lead to a lot of comments about how it's still buggy and "in development" for the 1.5 version of KSP. If I'm wrong and there's a good, safe download for it, please let me know
For others, I'm referring to this comment here:
The issue was that command pods didn't get recovered, for some reason. They seem to be working now, when I trimmed my mod list down to just Scrapyard, MagiCore, and Oh Scrap! (with the Kerbal Changelog installed too,because of Oh Scrap!).
At this point I'm going to assume it's a mod conflict (or possibly CKAN being idiotic), but due to a few issues (with CKAN) during the process of stripping my mods out for testing, my mod install/setup got completely wrecked so I can't even give a proper list of the mods present at the time this was happening. Which also means I'm gonna have to spend the next hour or two trying to rebuild my mod list, whee.