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I know right, my guess is that the execute command runs later or at a different priority. I found the suggestion somewhere and it worked. I didn't have the issue on my local install so I never delved into the how and why it works or what was wrong.
I couldn't figure out what was wrong, so I did some digging through the plugin file system, and found a file that had been edited 3 days after downloading the plugin (last mod date was the key). At the bottom of one of the files I found the culprit! au BufWritePost *.tex silent call Tex_RunLaTeX() from Vim tips wiki
Ah right, gotcha. Depending on how much effort you want to put in and how perfect you want your solution to be it's fairly damn close. Every time you hot the bottom you cycle windows once with <C-w>w and continue next-ing till you hit bottom etc. But from the functionality you're looking for I do concede it doesn't seem to answer your question. Maybe further clarification in your question in future would be good? Be specific in what functionality you would like or what you're trying to achieve.
When you say you can't use the clipboard do you mean you can't copy paste like normal (ie with Command+C) or can you not access the clipboard with the +register?