Tx for the pointer Thierry.
So, I did a small script (because there were 314 methods) to see number of non-class-extension methods with and without loading the dirty marker package and I could spot the culprit.
Running this script before and after loading the second package and doing a difference on the two sets shows determining the overridden method.
methods := (RPackage organizer packageNamed: packageName) definedClasses flatCollect: [:class | class ��methodDict values].
methods := methods select: [:aMethod | aMethod category asString includesSubstring: '*'].
regards,
usman