Could be any number of things, but if I had to guess, it's either silt from the hydroton (not very likely, but I still get silt from my perlite on occasion) or precipitate from the nutrients and additives (more likely, especially with the extra alkalinity from the additional pH up and pH down. Keep in mind, not all soluble compounds are 100% soluble.) If I had to hazard a guess, I'd say watch the plants and see to it that they're doing okay. If they start doing poorly, go ahead and change it out, once with fresh water (flush your media), then the next day with proper pH balance and nutrients. See if it happens again.

You say you are keeping your ph at 6.0? That maybe too high. I like to set mine at 5.0-5.5, and let it drift up to around 6. Too high of a pH can cause some nutrients to precipitate, which will float or sink in the res.

Also, it is my understanding that pH up and down should not be used at the same time (can't find the article on this). If you overshoot your ph, just add more tap water.

I'm growing mostly peppers and tomatoes. From what I've read, the pH should be in the 5.8-6.2 range otherwise I risk nutrient lockout. 5.0 seems like that would be on the low end? I'm concerned if I set it that low I may be hindering their growth.

I'm also curious.. if these are salts/nutrients dropping out of the water, if I add more tap water to my reservoir, will that allow them to dissolve back into the solution?

IF there are nutrients coming out of solution, adding more water won't likely get them to dissolve nor is it likely caused by pH. Normally, nutrient lockouts occur when you combine nutrients in too concentrated a solution and some of the chemicals bind with others before the water can "get in the way" and prevent it. At that point they are bonded at the electron level and adding water won't separate them.

Could my problem be caused by bad tap water? I was filling 5 gallon bottles and leaving them outside in the sun.. but I found out last night that in my area they add chloramine to the water and not chlorine.

I haven't read the original post yet, but just wanted to say that precipitates can most certainly be caused by pH. However from the reply's I have read, you try to keep the pH lower than normal, and precipitates are generally caused by pH that is too high (above 7) or bad nutrient mixing/concentration practices. I'm not sure exactly but I think it can be caused by extremely low pH as well, like below 4.5 or so. Water quality is always a concern in hydroponics. Again I haven't really read the original post, but here are a few articles that may help you figure things out:

Hydroponic H2O: Water Quality and Treatment
Water Wisdom For Hydroponics
Keeping Roots in Tip-Top Condition
Oxygenate,Respirate or Suffocate
Moisture Matters
Nutrition Solution Problems
Nutrient Solution Problems (Part Two)

Sorry for the long list, I know it it's a lot of reading to do, but hopefully some or all of it will shed some light on your issue, or at least point you into the right direction. Even if not, it's all good information everyone should know. I'll try to read the original post soon.

Also nutrient nutrient lockout (not precipitates) can be CAUSED by "precipitates" because they bind up the nutrients as grizz mentions. But it can also be caused by an unbalanced nutrient solution. Knowing the EC/PPM/TDS wont be able to tell you if the nutrient solution is balanced (and thus why I'm not concerned with EC/PPM/TDS readings like most people are). They readings only tell you the relative strength, you still need to know the concentrations of each mineral salt to be able to make determinations of deficiencies and/or toxicities. That's only done by lab testing, or guessing (based on symptoms).

Nutrient lockout can be caused by deficiencies and toxicities, as well as precipitates (because precipitates cause nutrient deficiencies). Precipitates are caused by bad nutrient mixing practices, high (passably low) pH, and/or poor water quality (bonding/binding with excess minerals in the water supply). Like grizz also mentions, adding water to the solution wont redissolve precipitates, they'll remain bonded (thus unusable to the plants).

I decided to suck it up and buy some RO water from an aquarium store for $.50/Ga. what inspired me was a water stand that claims to be a modern water pumping station that filters the water 6 different ways which also included UV, Charcoal, and Reverse Osmosis(all for $.25/Ga).

The TDS reading was 63ppm after I finished adjusting the pH to 5.4.

I let it run like that overnight and the water was still crystal clear today. I'm going to run my system with this fresh water for a couple days to flush the system and settle things down.

I greatly appreciate linking me to those. I have a thirst for knowledge and always look to augment my own experiences as much as possible by reading.

The discoloration is because of root decay. The chloramine is combining with iron in your water to make that silt.

I just wanted to post an update to my thread. After switching to RO water, I no longer have had any buildup or nutrient fallout in my reservoir. The water has remained clean/clear (minus the coloration from nutrients) for a week now. I did find that my pH was bouncing up unusually fast. After some troubleshooting, I found that was caused by the organic pH down I was using. By switching back to General Hydroponics pH Down, the pH has proved to be much more reliable.

1) Use RO water, the chloramine/iron and other things will have reactions that will cause stuff like you are observing. Start with clean RO water.

2)5.5 PH is too low, especially if you are growing tomatos or something. 5.9-6.0 is the appropriate range. My tomatoes like it a little high, at 6.2, but I usually drop it to 5.9 and then let it drift up to 6.2 before correcting it. Since I started using RO water, I don't even really have to adjust the PH, it starts at 5.9 and takes more than a week to get to 6.1