dont know if it works the same as iphone but you could restore your ipod to factory then try the jailbreak again, very odd issue you got there.
also as far as im aware the 5 rows accross the top is not a standard feature of the jailbreak, so sounds like its one of the packages installed by cydia, in which case you could try removing the package and putting it back on.
i know you can get a 5 button dock and the rest of the springboard stays the same but not heard of it the other way around