Although I would still recommend upgrading (both the Zen Cart version and the supporting software) I would at least recommend upgrading the SBA software.
While I believe the "time" since making changes issue brought this to mind, may I suggest taking a look at the sequence of the option values and corresponding option name's attribute value for variants known to work against those found to be out-of-stock.
Previously the sequence of those attributes had to be set/reset after generation so that they would work properly. The more recent version doesn't get hung up with that and offers some additional options. Available:
https://github.com/mc12345678/Stock_...butes_Combined
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