Flashgot was not automatically intercepting any downloads. Had alternately enabled "Autostart downloads" with "Intercept all downloads" - tried " File Extensions"
I was able to manually pass downloads to Free Download Manager using "FlashGot Link" and FlashGot Selection" or using ALT-Click
What worked was uninstalling other download related plugins: Free Download Manager plugin, DownLoadThemAll and and incompatible plugin whose name I forget but it may have been "BatchDownload" which for some reason had not got updated
I guess it pays to not trial too many plugins at the same time
Spec
FlashGot 1.2.1.23 on Ffx 3.6 on XP sp3
Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.2.3) Gecko/20100401 Firefox/3.6.3