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Water Colored

I haven't posted in a while.  I am a newbie, lurking and learning.  I am 
amazed at the knowledge shared on the list.  I don't have a lot of the 
equipment mentioned here.
I have a 29 gallon with a power filter, double strip light (2 x 20 watt 
bulbs).  I keep the water soft (proper pH 6.5).  I changed my substrate a 
week ago, from gravel to new gravel and laterite.  The water was very dark 
yellow.  I thought it was coming from the new dark brown driftwood, purchased 
over a month ago.  I soaked the driftwood for days and it bled.  Anyway, when 
I changed the water last week, it was clear and the tank was so much 
brighter.  Now, I noticed the water is darkening again.  I do use Florapride 
by Tetra.  Is it the driftwood or the liquid fertilizer changing my water?
If it is the wood, what can I do about it?  

Also, my crypts are not doing well since the change?  There has been a lot of 
dead leaves and they are looking pretty thin.  Is there a reason for this?  
They, as well as all my other plants (except swords) were doing fairly well.  
I bought root tabs, for my sword problem (as advised here).  What should I do?

Any advice for the newbie?