This is a known issue with the JMicron drivers, at least a few months ago, not sure if there are newer ones avail now?
The solution was to let Windows use it's own driver "Standard Dual Channel PCI IDE Controller" Either delete the JMicron controller and "find new hardware" or use the "update driver" option and pick it from the list.
I had the same prob and read about the solution at the Xtreme Systems Forums but can't find the exact thread now. At the time I was running XP and after changing to the above, the slow boot was history.
Since then I have used Vista x86 and currently Vista x64, both installs automatically used the above driver and my Plextor DVD-RW works fine.
If you use the eSATA function of the JMicron then the above solution is not an option unfortunately.