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Sorry, not follwoing much of that. What is a "hanging read"? What are "..other synchronous calls ..." There are no synchronous data service calls in Flex.
What RPC protocol are you using?
I've seen issues with having multiple ModuleLoader's run at once on start up (more than 2 and it randomly picks which ones actually run), so it certainly seems plausible there might be issues.
I've heard people use multiple domains to get around the per domain connection limit in some scenarios (not for flash/flex, but in general). Ie. have your network people point regular.example.com and hanging.example.com to the same thing, and use the different domains to get around the limit.
This is all using web services (and the <mx:WebService> tag). A hanging read is similar to a poll except that the waiting occurs on the server side. For example, it might be configured to return after 20 seconds or if some event occurs, whichever comes first. The client then makes another call when the previous one returns, thus giving the same effect as a poll but providing more responsiveness (at the expense of keeping a connection alive for the life of the client).
I experimented with this by separating out our two components, each with a hanging read as well as a set of other operations which can be called in a normal synchronous fashion. What I found was that "normal" calls seemed to get placed in some internal queue before actually being sent out. My evidence for this is that I observed a noticeable delay after calls to <operation>.send and before they arrived on the server. This delay seemed pegged to the timing of the hanging read going on in the background.
This occurred in browsers with shared sessions (2 Firefox tabs, 2 IE Windows with the 2nd started with File->New Window). However, when I tested with two independent IE instances, it went away. My conclusion is that, behind the scenes, Flash is putting these requests on the same queue whenever they are part of the same HTTP Session. I'd love to hear from anyone else who has experienced this behavior.