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Found one possible cause for some families not loading. If the annotations being collected for the leaf nodes (experimentally determined) were made to obsolete GO terms then havoc ensued. PAINT now courteously replaces the obsolete term for these experiment annotations with the replacement term. (If there is one and only one replacement).
As a by-product while debugging the above the matrix term-column sorting was sped up. Perhaps not an obvious improvement, but slightly less waiting time.
Restored the older version of macify. May help with the qualifier dialog box not showing up. Please let me know.