Gord,
The four hour contact time for the Katydyn Micropur tablets is required only if Cryptosporidium is present and is the same contact time, or less, than required for Crypto with all other water purification chemicals. For most other organisms, the contact time is more on the order of 15-30 minutes depending on temperature.

The free chlorine released from the tablets acts as a bleach and is the likely reason your water lost some of its organic color; pretty much the same thing that happens to skid marks on underwear when you use Chlorox. If you have heavily colored water with likely contamination, I would use a double dose of the Micropur since some of its anti-microbial potential is used up in making the water pretty.