Hi Lil1
Thanks for your post. Allowances are reported separately in STP so are not included in the Total Gross amount. For your other issues I'd recommend checking if the Payroll activity and Payroll register reports are the same. This post, AccountRight reports don't match STP reports, has detailed information on finding and fixing any issues.
This post, EOFY FAQS and Resources, has links to posts and Help Articles that you may find helpful.
If you continue to have problems with reconciling payroll please feel free to send me screenshots of the Payroll activity report, Payroll register report and YTD verification report by private message.
If my response has answered your enquiry please click "Accept as Solution" to assist other users find this information.