I had the same problem with Prohosting. I do believe it's the banner ad that is messing everything up. I had read through their help files and they said that the ads do sometimes mess up javascripts ???
Greymatter works fine on Prohosting, but you won't have all the features MT has :(
There was a suggestion in the Prohosting help files about putting the javascripts on separate files and then linking to them. I don't know whether that would work or not with MT