This was not a show stopper, however I think it might be an unintentional behavior in how 1Password is parsing the TOTP URI from QRs / pasted in URIs.
In setting up OTP (using TOTP) with FreeIPA v. 4.1.4 I kept experiencing problems with 1Password's scan of the QR code (it would create a URI, but the TOTP would not work). I tried pasting the URL manually and experienced the same thing -- so I experimented with removing different parameters from the URL (since many were "defaults" and not necessary to the URL). I was able to make it work if I removed the algorithm parameter and it's value from the URL.
Out of curiosity I noticed that FreeIPA is sending algorithms in lowercase, not uppercase (like some implementations of TOTP seem to expect, I'm not 100% certain if the RFC spec requires upper/lower or is case insensitive). I was able to get 1Password to work successfully when I changed the algorithm parameter's value to uppercase (i.e. &algorithm=SHA256 instead of &algorithm=sha256 ).
If it's not a violation of the RFC spec, it might make 1Password's TOTP more compatible to not be case-sensitive about fields where case isn't really relevant anyways.
Either way, I love the product and keep telling friends and co-workers about it!
1Password Version: 5.3
Extension Version: Not Provided
OS Version: OS X 10.10.3
Sync Type: Not Provided