Weird PMT Signal: Help!

For a start, most pmt's will give a negative output.
secondly, you are using a monochromator to view the light signal....so in effect you are allowing nearly all of your laser through unto the pmt.....
the rated wattage of your laser is 200mW and its seeing nearly all of it with the exception of the small sidebands you get with lasers and how well they are tuned....
your pmt at that power is absolutely bound to saturate in my opinion......

consider that if you had a small light source running through your monochromator, then the power would be distributed amongst the differing wavelengths.....here you are confining the power to less than a few nanometers....

looking at the datasheet for the type...
http://209.73.52.252/assets/pdf/parts_R/R928.pdf

i'd say that you have exceeded the max power per lumen that the anode can deliver which would cause saturation....

The quantum efficiency of the wavelength would make it less because of its peak at 400nm...the chart reveals somewhere around 55%, really its less as at 400nm is not quite a 100% so it would be best to do the ratio properly but i'm just doing it roughly....

from here we can see how to calculate the maximum input wattage.
http://books.google.co.uk/books?id=...=9TSE4i6tZsK3Cip1-JFTWuC-c24&hl=en#PPA286,M1"

which is the anode current divided by the maximum anode sensitivity (radiant)
= .1/(roughly 500000) = 0.2uW

and you are using 200mW......

chopping is not going to reduce the power.....just the time spent....

i'd consider trying to either reduce the beam power by using a beam splitter or going for a lens and spreading the beam somewhat in front of the chromator.
To tell the truth, a beam splitter might only bring it down to 5% which is still much higher...
maybe by scatter would be a decent solution??

hope this helps.