If you changed the cylinder regulator and the problem changed, but then reappeared, what action may have solved the problem?. I'd want to investigate that issue closely.
Does the problem go away if you turn the gas off and then back on. That would suggest a pneumatic cause, such as suggested by Gasman.
What sort of flow control do you have for the Detctor gases. If there are single stage regulators on the detector gases on the instrument ( rather than needle valves ), one of those could be misbehaving, or affected by the ambient environment.
I would certainly want to vent the ECD into somewhere other than the oven - at least for testing, and all ECD detector vent lines should follow manufacturer's recommendation. Just ensure that you follow their recommendation for any vent line internal diameter and length as well.
Are you sure the negative peaks don't correlate with some change in ambient conditions - ensure the conditions are consistent. If there is anything that cycles, such as air conditioners, ensure the negative peaks don't correlate with ambient temp/press/humidity changes.
One common device that is often overlooked is the printer, many of which have heaters, and some of which cause effects on the electrical power circuits.
Vibration can make intermittant connections misbehave by slowly increasing electrical resistance, and then suddenly return to the original state. All sorts of peak shapes can occur, and minor thermal changes or other environmental changes can easily exacerbate the problem.
Also, if the detector is not well insulated from the oven, you could try putting a little alumina wool in the oven below the detector to ascertain if the problem is thermal from the oven.
The obvious question, belatedly asked, is has the serviceperson for instriment manufacturer offered any suggestions. If it's a problem with the instrument, they may have encountered it previously.
Bruce Hamilton