Hi there

From what you describe:  It sounds like you have your expression pedal assigned to both your Wah and to your Amp Volume level.  You would therefore want to remove the assignment from the Amp Volume level.

I don't know which Pod HD you have but on the POD HD500 with HD Edit you would:

1 - Select your patch.

2 - Select the 'Controllers' section.

3 - Under 'Model':  select the amplifier that you are using

4 - Under  'Parameter': select 'CH Vol'

5 - Under 'Controller':  select 'Off'

This should remove the Wah from the Exp1 pedal.

Now, to fix the sound of the Wah, there are three things I suggest

A)  Make sure that you have selected a Wah Model that sounds best for you. The default is 'Fassel' but one of the other models may sound better. Try 'Weeper' or 'Throaty'.

B)  If your Wah is sounding 'too trebly' or with too much high freqencies:  set the 'Minimum' and 'Maximum' for 'Position' for the Wah under controllers. This sets the lowest and highest frequencies that the Wah will reach.

1 - Select your patch.

2 - Select the 'Controllers' section.

3 - Under 'Model':  select the Wah that you are using

4 - Under  'Parameter': select ' Positionl'

5 - Under 'Controller':  select 'EXP-1'

6 - Now set the 'Minimum' to the 'lowest' frequency that you want the Wah Pedal to go to and the 'Maximum' to the 'highest'.

C)  A final tip.  As default, the Wah is set so that 'Mix' - the balance between Wah-ed and unaffected sound - is 100% Wah.  Can I suggest that you turn the mix down to around 60-70% so that the tone includes some of the unaffected sound.  To my ears, that sounds a lot more natural.

If you are not using HD Edit then please come back.  Also, make sure you have a copy of the advanced guide for your POD, available here:  http://line6.com/support/manuals/