~What type of medium; soil or hydro?
Soil
~What brand and type of soil?
50% MiracleGro Moisture Control Potting mix (N/P/K 0.21/0.07/0.14), 50% perlite.
~What strain?
Seeds saved from unknown "headies" buds.
~How old are the plants?
13 days (seedling phase).
~What type of lights and how many watts?
three 42w compact flourescents @ cool-white 5100K.
~How far from the lights?
~4 inches.
~What, how much and when was it fed? NPK?
no liquid fertilizers added; only slow-release fertilizer from starter soil. A 1/4-of-minimum-strength micronutrient solution (Botanicare 'Sweet') was added yesterday to try to fight this issue of brown patches (described below).
~What are the temps and humidity in the room?
temp 71-79 F (hits minimum at night, when the house's heat goes down).
~What size pots?
regular solo-cups (~24oz?)
~Watering schedule?
Watered to saturation with room-temperature tap water roughly once every 3 days (whenever the pots feel light enough that they seem dry). Tap water in the area (a major US city) is considered great quality and is drunk regularly by local residents.
~Experience growing?
Experience with one previous grow that reached several weeks into flowering looking moderately healthy but the project had to end early.
Additional info:
3 days ago new growth was looking a significantly lighter green than than older leaves; this was assumed to be the beginning of a Nitrogen deficiency so a layer of 100% MiracleGro soil was added on top of the 50:50::soil: perlite mix to provide a small nutrient dose and fill the solo-cup pots up to volume with soil. The next 2 days saw remarkably increased development of leaf size and new growth, suggesting the plants were indeed in need of some fertilization.
The fans (two of those standard black Honeywell fans) were recently rearranged to the set-up in the picture, which changed the temp range from 79-85F in the first 10 days to 72-81F in the last 3 days (better air cirulation made the grow room adopt the temperature of the house it's in). The breeze from the fans is so strong it makes me wonder if it's a problem, though most of the plants can support themselves without the aid of a stake even in the strong wind. Temperatures have been observed using a cheap digital thermometer that records max and min temps.
pH was measured with acid-detecting pH paper (all that was available). This confirmed that the tap water, the Botanicare 'Sweet' micronutrient solution, and the runoff were not acidic (though the acid-detecting pH paper cannot test for alkalinity).
THE PROBLEM:
Yesterday faint patches of what appeared to be brown-colored lesions appeared at the bases of leaves midway up most plants. Not all plants exhibited this but, while it is believed all plants are the same strain, there is a chance they are not all the same strain.
Today the patches are clearly visible as slightly-recessed (like a water-mark on paper) brown splotches between leaf veins and mostly localized to the bases of leaves, though some leaves have the brown patches near their tips. I've looked long and hard but can't find any indication of pests or other obvious mold or fungi (unless this is mold or fungus). Also, leaves seem like they may be a little droopy but the plants are so young it's hard to say what normal leaf posture is yet. I suspected a micronutrient problem though now I am afraid overwatering may be the issue; I've been checking to make sure the pots become as light as is possible and stay that way for a day before watering, though.

Picture 1: The overall setup.

Picture 2: Brown patches at leaf base. Some leaves have also begun showing similar patches near tips.