After applying the most recent mandatory patches, I came across these issues and fixes:
1) Mandatory patch 5644830 was missing pasb038.drv. This is fixed by applying 3485155 first.
2) Refer to the CUP1 preinstall patches – see MOS Doc. ID: Oracle E-Business Suite Pre-install Patches Report (Note 1448102.1) to get all the latest mandatory patches.
3) Use patchsets.sh to find the latest family packs that include the following patch for Desktop Integrator – Oracle Web Applications Desktop Integrator 12.1.3 Release Update Patchset 1 (Patch 9790225, R12.BNE.B)
4) Patch 9577274 will have to be applied to fix the issue for the EBS login which gives the APP-FND-01564: ORACLE error 6550 in afpoload.
5) Apply patch 9535311 to all applications tiers, create the appsutil.zip with $AD_TOP/bin/admkappsutil.pl and copy to the database server to resolve application security issues with mod pl/sql. See this note: Why Does Autoconfig Fail On 11.2 Database ORACLE_HOME? [ID 1058815.1]
Apply the latest TXK patch which includes the fix, using the corresponding patch for the respective version of EBS.
Release 12.1.x – Patch 7651166
Release 12.0.x – Patch 9386653
Release 11i – Patch 9535311