Q: prohibitory sign but everything checkout fine

two days I was presented with the Prohibitory sign during boot up. I searched for the forums and google around, but no one presented the same case.

while prohibitory sign was present, i was able to boot to safe mode, backed up everything. diskutil showed no problem with the hard drive, except partition map problem but diskutil did not fix it.

henceforth, I tried to boot to single mouser mode, but was presented with kernel cache error 0x6

I booted back to safe mode, and everything was working fine.... decided to formate and wipe everything. but before that, I did hardware diagnostics including the extended version, but without any sign of hardware problem.

decided to formate the HD and reinstall el-Capitan....

installation was done, booted normally, set up my mac as new. rebooted again to check if everything will boot fine, but the prohibitory sign showed up again. booted through external hard drive, and performed first aid, and it booted again fine.

rested the PRAM/NVRAM and reset the SMC but without any change.

I am not sure what is wrong it, especially that single user mode present with kernel cache error 0x6

Additional information, five weeks before this problem presented itself, I tweaked the EFI to boot as black screen with apple logo instead of the grey one, with mac-forum/github forum.

P.S. I am writing from this same Macbook pro mid 2012 that is dealing with prohibitory sign.

Any help would be appreciated.... right now, the macbook pro is clean install with nothing installed on it, including third party softwares