In the In-Portal 5.3.x branch we've moved away from Swfupload solution in favor of Plupload ( - INP-1331Getting issue details... STATUS ). In turned out that we've made small mistake in way how we applied our restrictions on top of Plupload.
We validate maximal allowed number of files, that user can have in a single form field. We've implemented this in Plupload event, that is triggered after file is added to a queue and then we remove it from queue when needed (e.g. http://stackoverflow.com/questions/15513689/jquery-plupload-restrict-number-of-uploads/15520225#15520225).
In retrospect that was wrong way to implemented and we should have used File Filters instead.