If you haven't noticed, URC's favorite motto: "There's a work around for that." Well, not always apparently!  Seriously, this problem is nuts!

I didn't read the entire thread, but I'm sure you tried having all of the macros programmed in the MSC400 and triggering them with the remote? This should speed things up (it does for my MX-900s).

I've only used the MX-900 remotes. I've had the repeat issue (there's a work around for that) and a strange issue where RS232 commands would drop 2 out of 5 consecutive presses. I found a work around described in this thread (no thanks to URC, I had to figure it out myself):
[Link: remotecentral.com]

With my work around, using triggers on the MX900, I can press a button about three times a second and see a response on the RS232 port! The remote is NOT that responsive if I just use regular MX900 macros alone.  If it didn't work this fast, I can tell you as an end user, the remotes would be on ebay!

If you're curious, I don't use the MSC400 for IR, but instead have the MSC400 send a custom RS232 protocol I designed for my home automation system: [Link: cocoontech.com]

The only problem I haven't found a work around for is every now and then, I'll hit the light button and the light doesn't come on the first time, unless I hit a button first. This may be by design (to avoid accidental presses of the light button), but is annoying.  The issue was documented on here previously (many years ago), and it's good to know URC still hasn't fixed it!

Now it's time to rant more about URC:
How can URC tout a product as "professional" and not be able to get something so simple right?!?  I'm glad I'm not the customer or the integrator in this situation.  Anyone paying $500 plus for one of their remotes must be misinformed or out of their mind to settle for a one second delay between simple commands.  Their engineering team must have seriously fired their good talent, because a remote is not that hard to design and get right the first time!

As a dealer, you may not want to hear this, but...  The only reason I use URC myself is due to the large supply of cheap used items on ebay and cheap new remotes from other online sources; plus I can heavily customize the menus however I want.

I'm not affiliated with them, but Control4 is much easier to install, does more and costs much less.  I played with several of their demos (lighting, locks and AV).  The remotes are real two-way zigbee and only cost ~$150.  I tried to get the zigbee lock out of sync and I couldn't!  The commands were near instant too.  If they weren't so picky about dealer software, I'd be using their stuff.  While it may be true that most users couldn't figure the software out, there are plenty of folks with a technical background that can read the help files and program a system just fine.