Your reagents need to be made fresh just prior to use.

3 M NaOH

     0.12 grams of NaOH

     1.0 ml of autoclaved dH20

10M NaOH

     0.40 grams of NaOH

     1.0 ml of autoclaved dH20

40 mM Hydroquinone

     0.55 grams of Hydroquinone

     12.5 mls of autoclaved dH20

Bisulfite Solution

     8.1 grams of Sodium Bisulfite

     15 mls of autoclaved dH20

     add 1.0 ml of 40 mM Hydroquinone

     pH to 5.0 using 10 M NaOH (150 µL)

Hi,

If you are manually converting your DNA, the suggestion of Timothy is correct, since the bisulfite conversion will be highly impaired by old reagents.

Also for manual conversion make sure you clean your DNA thoroughly since the the high salt concentration will impair your PCR.

If you are using a commercial kit, the issue should be in your amplification step or in the way you store your bisulfite treated DNA.

Bisulfite DNA needs to be stored at -20°C for medium to long term storage (some people even suggest -80°C for long term).

+4°C is ok for several hours but I would not use this for longer period.

At room temperature your bisulfite DNA will degrade really rapidly. 

For your amplification, not all the taq will give you good results. If you can afford it, you might want to try another taq that the amplitaq gold. I used it in the past and also got an issue or reproducibility and specificity with bisulfite treated DNA.

After changing to platinum Taq, I got stronger and specific bands. Amplitaq gold is a good product for regular DNA, but I expect it does not like too much the low complexity sequences which result from bisulfite conversion.

Be aware that some taq does not use template with uracyles... the high fidelity Phusion Taq for example does not work on Bs-DNA. Also last point, if you change brand of taq make sure your taq does not contain UNG... 

I hope this is useful,

Best,

Tq Prof Donlon and Dr. Barault..