I selected several items and tried to join them using Ctrl+Shift+J.  (using 0.9.91b portable).

 

When I clicked OK, the top item disappeared (I lost the content in that item).  An error message appeared in the bottom right corner of IQ:

 

 

I experimented with different iqbases (sample file, empty file) and had the same problem.  I experimented with different versions of IQ, going back to 85a - same result.

 

Finally I discovered that the problem did not occur when I unchecked the "Delete Merged Item" box in the Join Items dialog.  

 

It seems that if "Delete Merged Items" box is checked, the top item to be merged is deleted before the merger is performed, so the merger fails.