Yeah, sounds like there is a big problem by the flashing lights you describe - that's not normal and seems like the remote is getting stuck on rebooting itself or something.

I have a 1000 and am returning it tonight, at this early stage it is just way too buggy.
Could never get the thing to work properly and for a remote that expensive, there shouldn't be problems like that.

I got an 890 instead and was able to program and get it fully tweaked within a few hours. I think that says a lot.