I am having the same problem:
I have a workbook that has evolved over several years, it is used like a
template, although it is actually just a spreadsheet, named template6.xls.
I recently made some apparently minor changes.
Afterwards, every time the workbook is opened I get one additional entry in
the project explorer showing an additional "vbaproject (template6.xls)" [so
far so good] but when I close the workbook, that entry remains. If I
open/close the workbook 10 times, I get 10. If I open the template6 and save
as a new name then the new name is what appears.
So, I removed (commented out) the updates. The new behaviour didn't
go away. I saved the bad workbook as template6bad.xls and printed out the
details of the changes.
I went back to the backup of template6 before the changes and confirmed that
it did not have this behavior. I re-implemented the changes. The problem
does not exist in the re-implemented version. I checked afterwards to see
that the problem still existst in template6bad and it does.
I have an addin that I use to process large numbers of spreadsheets but this
is a red herring - its't the way one runs into the problem, only an addin can
open/close enough spreadsheets to run out of memory and thus tell you that
you have a problem.
The problem occurs if the spreadsheet is opened and then closed. You
typically wont notice there was a problem unless you look. My guess is that
there is a "Garbage Collector" routine in Excel that is supposed to clean up
when a spreadsheet is closed and under some conditions can be made to fail to
do that.
Appears to be an Excel bug.