I take it you have just switched to 6.1?
There are a few er....minor glitches with the transfer...
If you are updating old QXP files, safest way to do it is copy it to your desktop and yes, do a save as...this will write you a new 'append file' (an invisible file contained within the QXP document). It will basically write a new QXP 6 file thus loosing all the old QXP4 or 5 tags.
Updating files in this fashion is by far the safest way...otherwise you may/will encounter some very strange problems...(missing text, missing placed images, corrupt files, basically, anything goes). But once they are updated...all should be good in your world. I have found 6 to be far more stable...good luck.
BD