The changes could to 1) the printer , 2) the check form settings or 3) the font setting.

1) For the printer, verify the paper size in printer properties (Start | Settings | Printers. Right click on printer and select Properties.)
For dot matrix printers the paper size should be Custom defined size 850 by 700 in .01 inches (8.5" by 7"). Sometimes this page size will be reset back to default size such are 100 x 50. For this reason it is best to create a separate printer just for checks with this paper size. In FN under Print Checks, select Printer and check the options to always use this printer.
For laser printer, use the standard letter size with standard letter size check forms.

2) The check form settings are saved with the data files so reinstalling the program will have no effect. In FN from Print Checks, with any check on the screen, select Change Settings. The Change Check Settings screen will appear for the check form this checking account is using. Verify:
the margins usually top 0 and left 0.
the size of form usually 42 rows & 80 columns
the location of each field and the stub. Note: row =0 will not print the field on the check.

3) Font can also be changed. With the check on the screen, select "Select Printer". Select Font. Verify the font. Normally Courier New, regular, font size 12. This should be a monospaced font with 10 characters to the inch with default Check Form Settings in order for the printing to align properly.

These are the setting that determine how the check is printed.
To isolate the problem try different situations:
1) Try different printers with the same checking account.
2) Try different data files with the same printer. If is fine on some but not others then the printer is fine but the Check form settings may be the problem.

For more info, refer to the help file or the reference manual for the Troubleshooting section at the end of the Check Printing in FN chapter.