As juan2320 stated - the HDD is too slow. This is an issue i've mentioned a number of times previously - but since us HDD owners are in the minority the issue hasn't been addressed. (I've since bought a 4gb stick!)
Basically when the firmware boots up it looks for the seplugins directory, the information about which plugins are enabled/disabled and the related PRX files - because of the delay due to HDD spin up times the firmware is unable to find the files and therefore assumes that you do not have any plugin's. This is why the seplugins won't work and i doubt the autoboot eboot.pbp will work either.
My suggestion (if anyone is listening?!?) was to add upto a 2sec delay on the boot up when checking for ANY files on the MS to allow for spinup. As follows:-
1. Check if MS files are contactable / exist - if they are/do then boot immediately as normal (with relevant settings).
2. If no files are found, loop around the check for 2seconds until either they ARE found (boot straight away) or are not (Boot after 2secs).
To prevent this from delaying normal users with no mod's it may be worth checking for a 'standard' folder rather than specific files? (eg if the PSP folder exists but the files are NOT found, boot normally)
Devs- let me know what you think.
HDD owners - sorry you're stuck with it as it is for now.
PSPSwampy.