Yes, and no. Lighting does make a huge difference, but there is a wide range of what is fine.
Incandecent lighting, as you either know or found out, is very hot. It wastes a lot of energy creating heat - and this can heat your tank more than normal. A nice warm tank can mean more algae (given enough light) and could mean less dissolved oxygen (warm water holds less). Incandecent light also tends to be on the yellow end of the spectrum - leaving out a lot of the colors that many plants need or like and much of the light that the fish use to keep their colors bright and vibrant.
Flourencent lighting can be adjusted with different bulbs to give you different color spectrums as well as intensity. This is a good thing. They impart little or no heat to the system.
If you mean that your biological cycle has gone crazy since this happened, then I would say that perhaps it had a bit of something to do with it, but most likely is not totally responsible for it. The nitrogen cycle does require a fair amount of oxygen to process the ammonia, and if the lights heated the water such that they did not carry sufficiant oxygen, then there may have been a problem. The fish, too, could be feeling the effects of oxygen deprivation if the water gets too warm.
If you are used to useing green algae to help in processing nitrates, and the new lighting turned the algae brown or failed to keep it growing and processing nitrates, you could be seing higher levels of that because of the light changes.
In the long run - a month or two, you could potentially begin to see color changes and lack of vibrant coloration in your fish without the proper lighting - but it is not an "instant" thing.
I am glad you have the original lighting up and running now.

It certainly is a pain when something fails to operate properly.