Is it skipping them because it thinks they already exist? What are your settings on the second tab of the import? How do you auto-fill the CI name (logical.name)? Do you use the number table? What are your steps for this? If you can give more detail, maybe we can find out the root cause.
first of all check if you are inputting data for all keys in this table. And as said IrisGeist you must recheck how are generated your CI ids. Maybe for the first time to check if the data is correctly sorted for import you should not use generation of the CI number from FC but add it to the loading file as well?
I am using FC with RAD name getnumb.fc to generate auto number for CI's. In second import descriptor file, i metion my FC name earlier it was giving error because id field in device table was character field an that FC needs number field so i changed it to number but still it's skipping adding data.
Why you dont want to try to import data with your CI ids. If you did everything as you described suppose there must be mistake in something else. can you attach the errors which system gives while not adding cis?