Hi Elias,
I have seen a similar issue a few months ago at an ex employer. In their case 301 redirects have been ignored!
So basically what happened:
- They had an older link structure which they have redirected to the new url versions (this happened around 2009-2010)
- After a "silence" period in affiliate marketing they have reactivated their affiliate programs and heavily invested in it.
- Because of no. 2. they have gained a lot of incoming links with the old links
Now what we believe went wrong is that Google could interpret this as an "accidental" 301 redirect because of the high number new incoming links to the old version.
As far as I know, when they resolved their affiliate links everything went back to normal.
It might be that your situation is a similar one to theirs.
I hope it helps,
Istvan

(psss, you can find his twitter account on this page: