CE5 Slow boot from CF but fast when downloaded

My project is a simple CEPC with most options taken out. The release nk.bin
comprises less than 11MB. When the target is connected to Platform Builder
via Ethernet, the image downloads in 9 seconds and comes alive 6 seconds
after this. When I put the same nk.bin on a Compact Flash card that boots DOS
in the target and uses the same loadcepc program to load this local nk.bin, I
see six seconds of "Section physical start" console messages and then nothing
for 90 seconds, when the CE OS finally comes to life. Serial debug output
shows a few initial messages but nothing during the 90 seconds. What could be
happening during this time?