not trying to judge, but why two tables with similar fields? But ot answer your question it sounds like the second import isnt being read as a CSV file and therefore is not using the "," as a field separator. Double check the second import script options and verify??
whatever the case One option to solve some of the headache is to import the CVS one time into a staging table, then import the records into their final destination tables from that stage table? The stage table then can be used to clean up the data by modify, add populate ID fields, delete bad lines or headers, etc... prior to final "import" to the destination table