@misterc,
Overly aggressive overclocking? Battery on the brink of collapse? It might just be possible that Thumb, running that little faster, combined with either or both of the two, might be pushing it just over the edge.

I don't know what you consider extremely long calls but I have used mine for calls lasting well in the excess of two hours with no heating issues. The only time my N900 got too hot was during large (read: several hours long) Modrana downloads, with the phone under the pillow.