Aquadonis, for the category ID mismatch issue, I double-checked my SQL statements in the back-end and they seem sound. Are you familiar enough with your server's administration panel to send me a database dump of the following tables
links
terms
term_relationships
term_taxonomy
I will double-check that all data is correct and run some queries on the data to see why I am not seeing any issues with my dataset.
For the pagination issue, I never intended AJAX mode and Pagination mode to be used together, hence the problems that you are seeing. I will have to investigate deeper to see if this might be possible.