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Well loss of parts in IS is a completely different clause. The reason being the weapons are mostly single function and need only minor compatibility issues. Something like rebuilding a broken tool and relearning how to use it. IS parts though require complete regeneration of the part. Probable nanotech adjustments, neural interface synchronization with existing upgrades and what not. This version is basically regrowing an atrophied limb.
The difference in regeneration speed stems from the data used. The separate weapon just uses the older data, but the IS integrated parts are continuously evolving and the lost part is continuously revised with theoretical upgrades. Actual adjustments aren't made so the part is better than it used to be, but really really buggy.
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