as ytou already thought, the difference in the speed betwen aMule ane eMule is probably due to the credits (much more has been uploaded on eMule as you said).
Yopu can take the credits files form eMule (backup aMule's just in case) by copying cryptkey.dat, clients.met, preferences.dat (look at
http://forum.amule.org/thread.php?threadid=1604&sid=&hilight=cryptkey+dat+clients+met ) into ~/.aMule diurectory.
aMule for windows is NOT working properly yet. so please don't use it, or not as a principle ed2k client, since it's buggy and under development yet. Ask the polish for a binnary since he posted one once (look at the win32 forums).
IF youy switch from eMule to aMule in win, you son't get ytour credits resetm but you'll have to move them to the aMule directory if you want your eMule credits to be used by aMule on win32.
I hope that all helped

Greetings!