Blightcasters are not immune to horrid wilting. In fact, some forms even take extra damage from it.
There is a lot of unknown information in your screen shots that could be affecting your damage. Looking forward to the videos so we can get a better picture of what is happening here. That being said, can analyze what we've been given at least some.
Baba Lysaga
Left = normal. right = nerfed
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Good news is we're looking at spell casting though it isn't fully clear as to what spells we're looking at in the second screen shot, but can tell a few things:
1. Different spells. We're looking at kill zones (areas with multiple long lasting effects dealing damage intervals). Different spells will do different amounts of damage but with this zoomed in view, all we're seeing is the damage type.
2. Spell critting. In the Normal version, your Call Lightning Storm is critting, no evidence of that being in the nerfed version
3. Debuffs. Looks like you weave in Quench to get some extra damage in there. Its possible, nay likely that we're looking at different parts of the raid where the party is more focused in the Normal were more debuffs are being applied.
4. Spell Snap Shoting. When a player casts a spell, it takes a snap shot of your character's stats and will use those stats for the duration of the spell even if you stats change after. For example, if you swap between a melee focused weapon and a spell power focused weapon. If you had your melee melee equipped you had 600 spell power and cast Call Lightning Storm, CLS will deal damage based on 600 power for its duration even if you switch to your caster weapon increasing your spell power to over 1000.
Not sure if this applies, but is a common outcome for those looking to mix physical and spell damage. Especially with those creating kill zones.
5. Difficulty difference. I'd hope that you'd were running the same difficulty in both of these tests, but for those that may be unaware reaper difficulty imparts a very large reduction to damage compared to non reaper difficulties.
Aside from that, there are some effects that are within the same range. The cold and bludgeon are both present, this is most likely ice storm and while the nerfed show lower damage they're within expected parameter. Unlike 566 vs 52 pts of acid damage. Which means that the acids are from different spells/effects.
Scarecrows
Normal Scarecrow 1 & 2 & 3
Nerfed Scarecrow 1 & 2
Well, good news is, its easy to tell the difference here. Normal you're using acid damage, nerfed uses fire. Different spells and different sets of spell power. The latter of which I suspect that your fire spell power is a good deal lower than your acid spell power. Also other factors, same as above, may also be at play. Your 5 digit damage is from a crit from an acid well which is going to be a best case scenario.
Conclusion
Unfortunately this is insufficient evidence prove that Dungeon Alert effects are being applied erroneously without provocation. Its possible the full videos will provide more details that may reveal more. However, it appears that you're not seeing reduced damage.
The follow up question is then...
What caused the huge time difference?
Assuming that there wasn't any difficulty difference... that players weren't sitting in the instance early)...
With the same party at play. There is a likely suspect for such an increased time. Puzzle rooms. Killing scarecrows out of sync and/or puzzles confusion is easily the biggest possible time sink in that raid. Especially if everything else was equal (since the screen shots revealed no major difference in damage was present)
Regardless... all of those should've been painfully obvious to you and your team if any of those were the problem. Anything more than doubling your time in quest would've been apparent as you were running it
Which if that's true, then I'm forced to consider that you're attempting to manipulate your data to fit your agenda. Considering your group's previous hysterics.... Its becoming really hard to give you the benefit of the doubt that you're being objective and reporting on issues in good faith.
Apologies. I hope I'm wrong about that.