Ammonia test kits often don't distinguish between NH3 and NH4+. They just give you a "total" reading. Therefore, if your API test kit turns light green, it only tells you that the combined NH3/NH4+ reading is approximately 0.25ppm. But it doesn't tell you how much of each is present.....
We know that at a higher pH, there is more NH3 present (bad), and at lower pH, there is a shift towards a higher amount of NH4+ (less toxic). So below is an estimate of the relative percentages of NH3 at different pH values.
At a water temp of 25C (77F):
pH 6.0: Approximately 0.056% of Total Ammonia is in the form of NH3.
pH 7.0: Approximately 0.56% of Total Ammonia is in the form of NH3.
pH 8.0: Approximately 5.6% of Total Ammonia is in the form of NH3.
To determine how much NH3 is present, multiply the above % by the reading on your test kit. For example: Your test kit turns light green (0.25 ppm).
If your pH is 7.0: 0.25ppm x (0.56/100) = 0.0014ppm NH3.
At pH 6.0: 0.25ppm x (0.056/100) = 0.00014ppm NH3.
Assuming that the nitrifying bacteria require NH3 to grow, then it makes sense to me that the lower levels of NH3 (which occurs at the lower pH) will slow down their growth (and stall your cycle). They simply aren't getting enough "food."
(Please note: These numbers are estimates, and assumes that ONLY pH is the only factor in the equilibrium shift between NH3 and NH4+..... But this will at least give you an idea of the relative concentrations in your tank.)
Note: The above was for those who scored a low value in Jaysee's poll. For those of you who selected a 10, read on. (Insert evil laughter here.)
I used the Henderson-Hasselbalch equation to determine the relative ratio of NH3 to NH4+ at different pH values: pH = pKa + log ([NH3]/[NH4+])
In the above equation, Ka is called the acid dissociation constant. All acidic substance, including NH4+, have these values. It's a measure of the extent to which the acidic NH4+ dissociates in water to become the basic NH3. The values are easiest to find for "room temp" which is considered to be 25C (77F). At this temperature, the pKa for NH4+ is 9.25.
Now on to the math: (Are you still rating yourself a 10 on Jaysee's poll?)
If your pH is 6.0:
pH = pKa + log ([NH3]/[NH4+])
6.00 = 9.25 + log ([NH3]/[NH4+])
The ratio of [NH3] to [NH4+] = 0.00056
Multiply by 100 to turn this into a percent.....
So 0.056% of the Total Ammonia reading on your test kit is due to the presence of NH3.
If your pH is 7.0:
pH = pKa + log ([NH3]/[NH4+])
7.00 = 9.25 + log ([NH3]/[NH4+])
The ratio of [NH3] to [NH4+] = 0.0056
So 0.56% of the Total Ammonia reading on your test kit is due to the presence of NH3.
If your pH is 8.0:
pH = pKa + log ([NH3]/[NH4+])
8.00 = 9.25 + log ([NH3]/[NH4+])
The ratio of [NH3] to [NH4+] = 0.0056
So 5.6% of the Total Ammonia reading on your test kit is due to the presence of NH3.
The above is in line with the pH scale, which is a logarithmic scale. Each increase/decrease of one unit is a ten-fold increase/decrease in the concentration of H+ ions. (H+ ions are what makes a substance acidic. More H+ ions = more acidity = lower pH.)