Seems to be somewhat related to JRA-9367.

Steps to reproduce

Option 1

1. In List View in the Issue Navigator, add a custom field to the list of columns.
2. Drag it left so it's not the right-most column.
3. Refresh the page and that column should disappear (as per JRA-9367).
4. Transition one of the issues through the workflow.

Prior to Step 4 above, the issue navigator looks like this:

Afterwards it looks like this:

The "Example" text is from the custom field that was added in Step 1, and is positioned in Step 2.

Option 2

This can also be reproduced when a custom field (with a single project context) is added to the issue nav with results from more than the original project

1. In List View (Issue Navigator), add a custom field (with a single project context)
2. Click on an issue (to get to the view issue page) that does not have a value for that custom field
3. Click back in the browser

This is what the issue nav looks like before:

After clicking back, the values in the column have been shifted: