Wait, are you using Adv and doing batch import of shape files and using a template there?  Or are you importing one field at a time and using a template on the "assign columns to import" screen? 

I was originally thinking you had the points and then were importing results from a text file. Ignore the consecutive delimiters comment. Are you changing where the template file is stored when you save it? I'd recommend leaving it at the default which goes into that project's data folder. Then also make sure when you're importing you are grabbing the same one from the same spot. 

I'd just try it w/ one attribute first. Import the shape file, assign one column to pH or something and save that as "pH". Finish through the import and then do the same process, load "pH" and see if it gets assigned.