I just also confirmed that Patch 2 has not fixed the issue. I ran a report that generates 46,973 rows and it takes 2'55" to pop up the save dalog. I did this from the dhtml viewer. the export works completely different depending on the editor or viewer that you are using. DHTML using export-Current Document-Excel 2007 or Excel. Either one produces same results. From Java Editor, choose save as, choose my desktop or my documents, save as excel and it even took a bit longer. 3;03'.
I am an administrator and put every watch on this that we have available. the only thing we see is a cpu spike but, it gets no where near 100% so it is not a cpu or server resource issue. This is something in the coding of 4.1 vs 4.0 or earlier versions.