Algae sounds like a likely culprit. Have you tried adding 50ppm of H2O2 to the reservoir? Are you plants mature and established?

What is the number of plants, plant species and reservoir size of your raft system?.
What is the number of plants, plant species and reservoir size of your NFT system?
If the species, amount of light are the same... and the plant load to reservoir amount ratios about the same... then you could expect both systems' PH to fluctuate similarly.

One fluctuating less and the other more drastially.... leads me to believe you may have hit the nail on the head with the algae being the problem.

Here is some info I found at http://www.simplyhydro.com/nutrient_problems.htm

"Some growers add algicide products into the nutrient to kill off algae and there are a number of these products on the market. However, since any product which kills algae, a form of plant life, can also damage young or sensitive root systems, care must be taken with the dose and damage has been known to occur. Algae will also regrow, very quickly after applications of most algaecide products, requiring more and more of the chemical to get good control. In a study carried out in Belgium on Algae control in hydroponic systems, it was found that many of the products tested for control of algae in nutrient solutions (Diazinon, Endosulfan, Propiconazole, Thiram, Ziram, Quinomanid, Irgarol-1051 and Hydrogen peroxide) were either totally ineffective in killing algae, or killed off much of the algae but were also very phytotoxic to the plants and causes considerable root damage. It was also found that dose levels of 50ppm of hydrogen peroxide was requited to control algae, but that this dose was too phytotoxic for young plants, although older plants survived this dose rate. Therefore, careful and selective use of H2O2 could be used on older, more resistant plants, but since H2O2 is a 'biocide' rather than an 'algicide' there is always a risk of root damage.

Other studies have found 'organic' algae control methods such as adding certain 'grapefruit seed extracts' to the nutrient will kill algae without harming the plants - this is a method used in drinking water, fish ponds, lakes etc and appears to work well. There could be the potential, in larger hydroponic tanks to use 'Barley straw rafts' as a means of algae control as has been proven to work in ponds, lakes and other water ways. However the best method of algae control will still always be prevention of the problem, so excluding light should be the main emphasis in systems with algae problems."

A little more info on using H2O2 with dosing information.

Taken from http://www.quickgrow.com/gardening_articles/hydrogen_peroxide_horticulture.html

4. How to use it.
   H2O2 comes in several different strengths 3%, 5%, 8% and 35%, also sold as food grade Hydrogen Peroxide. The most economical is 35% which we recommend be diluted to three percent before using, as at this high concentration it can cause damage to skin and clothing. When working with food grade H2O2 it is very important that you clean up any spills or splashes immediately, it will damage almost anything very quickly. This is extra important with skin and clothing. Skin will be temporarily bleached pure white if not washed cleaned. Gloves are strongly recommended when working with any strong chemical.

Food grade H2O2 can be diluted to three percent by mixing it one part to eleven parts water (preferably distilled). The storage container should be opaque to prevent light from getting in and it must be able to hold some pressure. If three-liter pop bottles are available in your area they are ideal for mixing and storing H2O2. There are twelve quarter liters (250ml) in three liters, if you put in one quarter liter H2O2 and eleven quarter liters (250ml) water in the bottle it will full of three percent H2O2 and the bottle can hold the pressure that the H2O2 will generate. Three percent Hydrogen Peroxide may be added at up to three ml's per liter (2 1\2 tsp. Per gallon), but it is recommended that you start at a lower concentration and increase to full strength over a few weeks. Use every watering even on fresh cuttings. For hydroponics use every reservoir change and replace twenty-five percent (one quarter) every day. Example: In a 100L reservoir you would add three hundred ml's (3%) H2O2 when changing the nutrient. You would then add seventy-five ml's more every day.

5. Where to get it.
35% food grade: called food grade because it has no toxic impurities
Of course your local hydroponics retailer, whom you can locate over the web at www.hydromall.com. Direct order off the web (there may be shipping restrictions on high strength peroxides). H2O2 is used to bleach hair so the local hairdresser may have a source. The local feed supplier may have it in small towns. Prices range from fifteen dollars per quarter liter to eighty dollars a gallon. One gallon will treat up to fifty thousand liters of water.

3%5%, 8%
Can be found at most drugstores or pharmacies, prices start at a less than a dollar for a one hundred-ml bottle that will treat one hundred liters.

Haven't had this issue in our NFT systems but we have in our swc. I had a reading of 10 the other day for no known reason. I got it down to 7 which is still unacceptable. This was rain water. I ended up using tap water as the best method of getting it more stable.

Thanks for the replies!
scfalconry,
I haven't tried using H2O2 yet, but i think it is a good idea. The rafts don't get any algae at all and are non-recirculating with no air stones. Both systems are similar size side by side in the same GH. Their is a few hundred lettuce plants in each system.
I will try the H2O2 to see if it helps control the algae and pH.

I have been using a small amount of chlorine added to the reservoirs but i think I am not adding it frequently enough.
Also, the NFT system has plants at different maturities. It is a perpetual system with nursery channels with holes spaced closer.
I usually try to harvest all the heads in a finishing channel at the same time so the channel can cleaned out and replanted.

The only problem with this setup is that it is hard to disinfect the whole system without stopping the cycle. I was thinking of using something like hygrozyme to help breakdown any dead roots and help keep the system clean.

Also, I am using town water with low dissolved solids.