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Blue Box Proto = Life Like before Walthers purchased them.
Silver Box Proto = Post purchase Walthers ownership
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Blue boxes had a clone of the basic Athearn drive. Silver boxes have the newer 14:1 helical gearing, a Walthers innovation. Gears & such are not interchangeable with Blue box locos. Some of the Blue box locos had the much discussed cracking axle gear issue, but not all of them. You won't find this in the newer Walthers models.
The Silver box Proto is not necessarily the Walthers version. My GP60s and SD45 are both Life-Like products with the old Life Like address and no mention of Walthers.
I don't own anything that new, but my contacts at Walthers told me that the silver boxes were introduced after Walthers bought Life Like, though they did keep the old name and even the old office. They still had three people at the old LL office up until very recently. I'll confirm this to be sure.
The SD45, as far as I know, only came in the silver box, and it has an odd gear ratio due to the compound gearing. The GP60 also only comes in the silver box and has a 12:1 gear ratio.
AFAIK, the gear-ratio-of-the-month thing was only done by Life-Like and not Walthers. Walthers has not announced any new diesel models in the P2K line that has odd gearing, and only re-ran models that had them. Of some of the models that had odd gearing, Walthers is actually regearing them (such as the GP60) for the Walthers release.