The change in FileMaker versions shouldn't result in a font substitution, so it's not clear why this happened in your case. (As a test, I modified some layout text to be Times New Roman in FMP 13, then closed the file and re-opened it in FMP 12, the layout text displayed as Times New Roman.
If this is data in a field, make sure that the data in the field hasn't been formatted as Arial as that will supersede a Times New Roman format specified for the field while in layout mode for the record where the data was formatted.
The form where the data is typed in, is Tahoma 12 pt. for the data and the field names. The report (for printing only) is formatted in TNR 10 pt. Works fine on my desktop, but the data and field names come up in Arial 12 pt on other desktops. Unless you have any other suggestions, I'll wait until we're all updated to the same version.
I have my doubts that the update will make any difference but the cause of the font substitution that you are seeing is unclear.