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What example sketch are you using? How are you powering the emonTx. Some cheap USB power adapters are very niosy which can result in problems http://openenergymonitor.blogspot.com/2011/08/not-all-usb-power-supplies-are-created.html

We are using the emonTx_onewire_temperature_Example.pde with some modifications to work with pulse counting...
It's not the best sketch because we don't have any CT-sensors... We are using temperature and pulse! Is there any better sketch for us to use with our configuration?

I think the problem started when we changed our pulse sensor from TSL257 to a TSL250 because we want it to be compatible to infrared! Do you think that could be a problem?

We have tried with different USB power adapters... None of them have been a problem before! Now we are using a Garmin USB power adapter for example.

It would be a good idea to remove the CT monitoring part of the sketch if it's not being used. It sounds like the problem is software rather than hardware. To prove this you could test the emonTx with the standard single CT sketch, this has been proven to be stable. 

The emonTX is now stable... Nothing is changed! We are running on the same sketch and hardware as before... Very strange!!??

A new problem has occurred... The pulse counting is peaking to 15000 watt and "lower" peaks sometimes.
Look at the picture. The only thing that is active is a heat pump... It operates between 600 - 1200 watt!

Does anyone have a clue why it peaks at 15000 watt etc.???

Bounce...

Please! Somebody?

Sorry Joskim, Im afraid Im not sure, Could there be any light from the surroundings causing spurious measurements? How well sealed is the sensor onto the pulse meter? The power feed looks very spiky in general, spiking down towards zero all the time, is this to be expected?