I am using:
PHPRunner 4.0 (build 241)
mysql Ver 14.12 Distrib 5.0.37, for Win32 (ia32)
I noticed that upon table creation if I don't specify an auto-increment primary key field before I save, I can't do it later. You can specify it through the UI but it doesn't make the modifications to the table. I got around this by modifying the table definition directly.