This has been discussed on the form before and another user labelled this behaviour as normal. However I believe it is a bug.
Basically: If you use the "replace footage" function, the alpha channel is reset to premultiplied.
Steps to reproduce:
1) Import footage.
2) Interpret alpha channel to ignore
3) Replace the footage file with a different one
4) The alpha channel is now premultiplied.
Interpreting an alpha channel to "ignore" is something that can only be done manually. If you've done it, you've done it for a reason. If you are dealing with a large number of files, eg multipass 3D renders, and you want to update those files to a newer version, you don't want all of the settings to be reset.
Using the "replace footage" function does seem to remember manual color settings, so having the alpha channel reset seems to be an oversight.