I recently had a perplexing problem with Google Tag Manager (GTM) and Google Analytics (GA) that I can't explain.
I track about 50 different websites. Each website has its own account and profile.
I also have one "aggregate / roll-up" account where its profile tracks all 50 sites together.
Then I created a new account that is also applied in all 50 websites. This new account was set to use Universal Analytics. I added its tracking code via GTM, where the same GTM container code is used in all 50 websites.
Immediately, the direct visits in the per-website accounts shot up by about 50%!
Strangely, when I looked at the "Hostname" report in the "aggregate / roll-up" profile, it did not reflect the direct visits increase. The increase was apparently limited to the per-website profiles only.
Once I disabled the GA tracking in GTM, my per-website profiles returned to recording "normal" direct traffic levels. During the affected period, I had not made any changes to the tracking code in any website nor changed any settings nor filters in the accounts and profiles. So it looks like there was something screwy in GTM+GA.
I had found a similar post in GTM's support forum, and added my experience there: http://productforums.google.com/d/topic/tag-manager/bRKRvti-upc/discussion
Does anyone know what happened?