This exact problem occurs for me as well, despite following the help file example to the point. I think that loops with alignments are still broken and doesn't perform as expected.
When I use alignments in loops (not the case of multiple parts !), I always save the alignment as an external one at the end of the loop, and recall it at the start (To do it, I have to play with alignment name to racall the previous alignment when the loop ID=1, and the last one when loop ID>1).
Hope this can help...
This exact problem occurs for me as well, despite following the help file example to the point. I think that loops with alignments are still broken and doesn't perform as expected.
When I use alignments in loops (not the case of multiple parts !), I always save the alignment as an external one at the end of the loop, and recall it at the start (To do it, I have to play with alignment name to racall the previous alignment when the loop ID=1, and the last one when loop ID>1).
Hope this can help...
