OK, I understand you problem better now. The initial explanation seemed to be opposite of what you were saying.
Sounds like you possibly have a corrupted / locked Cydia file. The file in question typically lives in the folders below var/lib/
The most common one to cause problems is var/lib/dpkg/status
But in your case it may be one of the others. It could be one of the ones in var/lib/Cydia
I would suggest using iFile to RENAME some of those files. Stick .bak at the end of the file name as a backup. Then try running Cydia again. Cydia should rebuild each file you rename and go back to normal. If it fixes the problem, great. If not, move onto another file and try again. If you get into trouble, rename the file back to it's original state by removing the .bak extension you added.
I would certainly start with the files in the Cydia, and dpkg folders. If you want to fastrack the process, try renaming the folders. Cydia should rebuild all their contents. If not, just rename them back.