So after extensive testing I've narrowed down the list of suspects potentially responsible for the heretical act of depriving me of my DoTs. 

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Suspect #1

100%physical dmg converted to warp psalm doctrine. (This unholy doctrine is also responsible for a lot of confusion amongst fellow inquisitors)

Damning Evidence

Removing and reapplying the doctrine lets me apply DoTs at the beginning of each mission. After a few kills they stop applying.

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Suspect #2

Berserk tokens, and  [+1 critical chance +1 crit strength per berserk token] item

Damning Evidence

The combination of these 2 things might be bugging out. The excess crit chance being added and the cap being 50% might be overriding something. 

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Suspect #3

To many buffs.

Damning Evidence

I can apply DoTs at the beginning of the mission, but once my buffs start stacking up they stop applying.

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Ive tried removing them, reapplying them, resetting, etc. nothing gives me back my DoTs. As an annointed agent of the throne, I request assistance from the tech-adepts of the Ordo Neocoreus in resolving this matter. I can not fulfill my Inquisitorial duties efficiently without this.

DoTs from weapons/skills that have the DoT tag are applying.

No worries sir, appreciate the reply.  I did try something else, I switched clients and started the game using the Martyr .exe instead of the prophecy. I was able to complete 2 missions with everything working fine, but when I started the third one it started happening again.

If anything changes, or I find a solution I will let you know.

Okay so after reading MerkeV reply, I tried this just now:

I logged in started a random mission, got halfway thru with everything working fine. Upon activating the innoculator, the chance on hit/crit effects stopped applying. 

My innoculator is using: 

+50% movement speed and remove speed debuffs

+10% supreme damage resist

+5% supreme crit +20 crit hit strength

+50% duration yellow components

I never even considered the innoculator as the cause, so I kept testing and switching out everything but the innoculator. I will do some more experimenting to see if it is the inoculator or not.

I can confirm that activating the innoculator does stop DoT/debuffs on hit/crit from applying, regardless of the source (passives/enchant/doctrines).

I tried these passives/doctrines/enchants, whatever the innoculator is doing it cancels them out.

Enchants 

- % chance on hit to poison/burn/bleed

- % chance to poison/bleed on physical crit

- % chance to burn on heat hit

- Bleed on crit (weapons)

Doctrines

- 10% chance to ignite enemies on heat

- All fleshbane attacks cause bleed

- Critical hits stun enemies

Switching weapons fixes it, until you use the innoculator again. This explains why it was "coming and going" and why it was happening on my three chars. 

MerkeV deserves the Inquisitorial Medal of Investigation, for pointing this out, because he has brought DoTs back to this grey dull world, and with it a renewed desire to purge the heresy from the sector.

Sure thing good sir, I will get to it and post results in a bit

So after a few hours of missions, it seems the innoculator is the culprit. The combination of components in the innoculator makes no difference, upon activation it will disable the characters ability to DoT on hit/crit. 

Switching weapons fixes it 100% of the time. Using the innoculator again disables them. So Im stuck in a cycle of innoculator use, switch weapon, since I use it for speed/defense/dmg buffs rather than healing.

And in regards to blind MerkeV I tried these:

Passives

Blind on DoT effect - works prior to innoculator, disables after use.

Weapons 

Assasin mace (forgot name)

Blind on hit - Does not apply regardless of supression state, or innoculator usage. 

I would test more weapons but blind on hit weaps are few, and I think theres a radical morality enchant for blind but it will take me a while to find one.

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On my Psyker I tried adding the blind component to spells, it applied as long as I didnt use the innoculator.

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So there is something going on with it to, not sure if its related 100% to the innoculator or not. Since on weapons it is not applying regardless of innoculator usage.

Yeah I changed the component.

And it was all MerkeV, I was off in passives and psalm codes land blaming all the wrong things.

And on a sidenote does several other things in the works mean more love for WH40k? :D :D :D :D