I can't believe that we're the only ones with this problem. Just try clicking away on some different s:links before the first click's response is rendered.
I don't believe this is a JSF problem, it's appears to be more of a seam problem (losing a handle to the conversation).
Any help from the seam guys (or anyone else) would be greatly appreciated.
First of all be asured that you're not the only one who encountered this problem.
In Trinidad e.g. they tried to solve this issue, by adding a block attribute to their commandLink and commandButton tags.
If you use ajax, then you also need to add a timeout that checks the state of the document (completed, etc.) and if it is completed than you need to render the layer invisible again.
but also let me add, that we haven't used this script in a long time, because the problems you describe seem to have already been solved in newer versions of JSF and Seam.
Seam 1.2 introduced a new concurrency model that probably solves this.