Hey Dan,
This may help:
http://omeka.org/forums/topic/problems-with-csv-import-plugin
Here's my best guess about what happened:
The background process did not have permission to read the file (the
column mappings does not use the php-cli), so the handle was null.
Since the handle null and was not checked, it got stuck in the while
loop which tries to read the file with fgetcsv, and this in turn
filled up the log with warnings.
I have since updated the trunk of the CsvImport plugin to check for
the file handle, so there should be no more giant log of warnings.
The next thing to do is to:
1) Use svn to get the CsvImport plugin from the trunk and install it.
(the forum link explains how to do this)
2) Find out which user the server uses to run the php-cli, and make
sure this user has permission to read your csv files.
If you can't use svn, we will probably publicly release an updated
version of the CsvImport in the next week or so with these changes.
Thank you for finding this bug and let us know if the problem is
fixed.
Will