without a detailed example it is hard to guess what is going on. Did you make sure that there are no filtering rules applied to the content? Maybe some things were still running in an embedded cyle? You could write a custom log file within the rule to verify this.
If this is not the case, I can only offer a wild guess:
The HTML opener can take up some resources and CPU time when he is checking for certain rules. Even if you have no rules applied but you call the opener he might look into web objects and process them. In case this takes a bit longer a progress page could be displayed. Flash and Ajax requests can't deal with progress pages and the site will break here, because the object won't reach it's destination. You can try to disable progress pages for testing and check if this helps.
If it does not we might need your configuration and an example to figure this out.