1 Create New blank project
2 Create audio track and drop an audio file into it at bar 4
3 Create ruler and set it to show timecode
4 Place cursor at bar 4 - the start of your audio file
5 Project -> Set Timecode at Cursor. Change start time from 0:00:06:00 to 0:00:04:00
6 The ‘You have modified’ box will come up - click YES
The audio has moved to bar 5 (6:00 on the timecode ruler). The ruler now starts at -1:23:59:58:00, and 0:00 is at bar 2.
7 Undo this - yes it’s called Modify Project Offset in the Undo menu.
Your audio file moves back to its original position of bar 4, however the ruler has NOT changed back - the audio is shown as being at 4:00 - it should be reading 6:00 again.
8 Open up the Time Display - it usually shows the correct time - 6:00
There are general problems with the ruler. For example, you can select what the ruler shows (bars beats / Seconds / Timecode etc) by clicking on the tracks title in the Track List window, and you can also select it by right clicking the ruler in the arrange page. In doing so, you can end up with Bars & Beats showing as the Rulers name, but with the ruler itself showing timecode for example. They are not correctly linked.
Take a look at this screenshot and tell me that this is all working correctly!
To correct this you can fiddle around with the ruler, altering what it shows, and eventually it will get it right. Also, as you mentioned, you can correct it by moving the cursor around the arrange page, but sometimes it takes a while to correct itself.