The main board is working with 5V supply and the POD uses the target voltage. Therefore, a level converter is inserted between the two systems. The extra logic and the level converters introduce a small, and for most of the time, negligible delay. Note that the voltage converters do not handle a +12V input voltage on the RESET pin which is used for enabling the parallel programming on standard parts.
After a power-up, the reset is forced active while configuring the AT90EM04, introducing a 1-10 ms delay.
See Also