This may happen with other liquid's (I'm guessing not water because it generates more source blocks) but I am using the latest pack.

I have tried moving it and resetting it and get various results.

It it fully power with speed and energy upgrades and I have tried without them as well. SameSame result but slower.
Powered fully and constantly flow of lava at all times via elite mechanical pipe and a gargantuum barrel of lava.
It pump's out swiftly and covers a good distance of what I want it to. But there are a lot of gaps where there is lava but it's not a source block.
Over a 200x140 area having so much flowing lava may cause issues.

I have reset it after its "complete = yes" for it to takes it time but eventually use a bit more lava fill in a few holes then stop again. Tried 4 or 5 times couldn't observe how much was filled in so it wasn't a lot.

Also moved it several spaces away to have it use a bit more than just resetting it.

If it matters I have it set up to pump between glass blocks.

Just recreated in creative. No obstacles just infinite lava and power.
It reached it max range and stopped but still there were lines on flowing lava in many places.

Maybe there is a configuration option to consider nome source blocks as empty?

I've made a hole (not 200*140 as you described in your first report) and it filled it perfectly, no hole to be found.

I have recently been using it again for several different liquids and a very very large amount of water. It seems it misses blocks out over a large area but not small ones.

I'm really no expert but I think it does checks of certain blocks but not all like the ranged pump for example is very uniform and pumps in a pattern.

The fluid plenisher however may create long lines of a liquid and then do miss a couple of lines completely. I can't work out a pattern if there is one anyway.

My latest endeavour was putting it against a wall that was over 100 wide 100 long and 20 deep. The results were ok it did 5 blocks wide and about 60 forward with a few holes here and there, I moved it to the edge of the side it stopped (5 blocks) and it did the same but 2 blocks wide.
I repeated it with different results every time.

I'll try and make the hole bigger. See if I get the same weird stuff.

Bigger hole (100 x 100 x 20 Damn markdown making it italic) and it filled perfectly in one try, no need to replace the fluidic plenisher or so.

That's crazy I don't understand what I could be doing wrong. I've tried on different versions currently latest. Currently on FTB beyond was on infinity lite.
Using a mekanism fluid pipe and a drum on top.
I can recreate it whenever

I can't reproduce this either. Perhaps another mod is interfering with the environment?