Hi travellers - I've successfully done harmala extractions from rue previously, but on this occasion I tried a few things differently and have some strange results. Hoping someone can shed some light on what is going on (from a chemistry perspective). Here's how it went down:

(1) Instead of grinding the seeds, I simply simmered about 350g in acidic water (vinegar+distilled water) and combined/reduced - partly because I'd read that the outer skin contains the harmalas whereas the inner skin and core don't, and also because I was going to try an alternative to the laborious filtering process
(2) Did some basic filtering, less than usual, just through a sieve and cotton
(3) Basified with sodium carbonate (the soup was a little darker than usual because of more gunk due to less filtering) and left it to precipitate/settle overnight
(4) I decanted the top basic layer and added distilled water, allowed it to settle then decanted again (repeated this a few times) - my thinking was that the freebase harmalas won't dissolve in water and that I could dilute and remove the gunk over successive repeats plus slowly reduce/remove the sodium carbonate in anticipation of acidifying again prior to the manske
(5) After repeating the above about 4 times, there wasn't enough sodium carbonate to precipitate the freebase alkaloids, so I added more and continued the process again - each time the top basic layer got clearer and with less plant sediment suspended in the solution
(6) Finally I decided to do the manske so I decanted the basic layer a final time and added a warm vinegar/water solution (by this time I'd run out of distilled water so just used tap water). Normally I'd run it through coffee filters and dry then acidify prior to manske, but I was trying a new (for me) approach. But the freebase harmalas refused to dissolve. I tried decanting and adding more vinegar/water, this time stronger. Still wouldn't dissolve. Tried hotter pure vinegar, three more times. No success, still a thick layer of freebase harmalas settled at the bottom. I tested the PH and it was about 6 - couldn't seem to get it any lower.
(7) Perplexed, I've just run it through a coffee filter and have some odd results:
(i) a fluorescent but quite clear orange liquid collected (looks amazing with a blacklight - see pic)
(ii) the harmalas collected in the coffee filter are dark PURPLE instead of the usual tan colour

I'm going to continue and see what happens, but does anyone know what happened here?

Your harmalas are probably dissolved in that clear solution. Try freebasing it using a strong solution of sodium carbonate, ammonia or sodium hydroxide.

Ive taken shortcuts before like not filtering enough or allowing time to settle after the initial boils, and it always led to more work cleaning up later on down the line. Whole seeds work fine though, but a lot of plant matter still comes out into the solution.

Yes boiling whole seeds suffices. I once did an experiment and gridning increases the yield by only about few per cent and it's not worth the efforn with extra gunk.

I would make sodium carbonate solution (I make 20%) or sodium hydroxide solution (10%) and pour that in while mixing.

My experience with freebasing by adding just powder or too strong of a base is that harmalas tend to clog and potentially trap impurities. Pouring in dilute base makes it smoother.

I also let the acidic soup settle before filtering as lot of gunk goes to bottom.

You can also use excess salt (15% or more) to crash the salted alkaloids from solution instead of freebasing it. Then filter it, then redissolve in plain hot water and then proceed with freebasing or Manske.

Thanks guys - both right.

I kept the re-acidified solutions that I decanted and luckily they still have plenty of goodies, although the manske only produced micro-needles. Interestingly, there were almost zero needles when I filtered the HCL crystals after overnight slow cooling (I was so disappointed) but then I noticed crystals starting to form in the filtered solution and filtered again. Voila! Over five successive filters the micro-crystals kept re-appearing until all done. Between filtering I stuck my collection beaker in the freezer and the cold glass aided rapid crystallisation.

The purple stuff turned out to be ultra-concentrated plant gunk. Somehow it coagulated into freebase-esque particles, which actually made it easy to cleanse the solution. I agree with blue-magic - it must have also trapped plenty of freebase harmalas because it they were clearly there early on, but over successive dilutions the plant matter latched onto them and formed heavy particulate. D'oh.

I might actually try a variant of this in the future, as it removed hours of initial filtering and concentrated the gunk into sediment that was easily removed, just need to find the right balance so that the freebase harmalas don't get irretrievably mixed into plant matter.