Welcome, @rjsoh
The Stringtie form has a default option to predict new gene models. You’ve already done that with the first round, and merged those together to create a new “reference”. Now you need to set the option to only use the existing reference data for the final gene counting round. This generates count that are all based on the same annotation, without more predictions, and all count files will then have the same number of rows (same set of genes).
Choose your merged GTF file, then find the option here on the form, and toggle it to Yes.
Xref StringTie error generating gene and transcripts counts files
Hope this helps! 