Bro... That is major overkill!!! you do not need to do a full wipe between nightlies...
I DO NOT USE ROM manager when i do this except for making my nandroid
all I do is DL the nightly I want(I use my computer and also load it to my phone from the computer). Then i do a nandroid backup of my current ROM (just in case

, then turn my phone off and then on into recovery mode (vol down and power button). then I flash the newest nightly, after that I wipe cache and then wipe dalvik cache, then I install the kernel again (you have to reinstall the kernel you want between nightlies for some reason)... after that just reboot and you are good to go. YOU def don't need to do a full wipe... maybe thats why your having so many problems dude ( i could be wrong about that) ... the only time you ever need to do a full wipe is when switching between two completely different ROMS... You are making soooo much more work for yourself brother...
when I flash I new nightly, it takes maybe 5 mins... I cant imagine having to reinstall all my apps everytime... Let me know how everything goes for you... if I helped; hit my thanks button