Hi hcpfinance
This has been on ongoing issue ever since STP Phase 2 when MYOB forced all files with payroll online. Users reporting the issues you are encountering are advised by MYOB to break larger payrolls into batches of 10 or 20 employees - totally impractical. However due to MYOB's systems and software coding, this seems to be the only way to make it work, it simply cannot process large payroll runs.
My suggestion - if you have more than 50 employees go back offline and use a 3rd party STP reporting solution such as STP Creator. Your payroll processing will return to how it was before STP - meaning you can process payroll for hundreds of employees in one go, much quicker, and you can freely delete and re-enter if any payroll errors are identified.
After you process payroll, you run STP Creator which extracts all the payroll data from your MYOB file and sends it directly to the ATO. Once setup it takes a few minutes extra per pay. Much less than you will spend splitting into batches etc.
Yes you would lose access to the file from multiple locations (if you need this) however many users are online only because MYOB requires it for payroll reporting.
Regards
Gavin