The stock flasher is deliberately sensitive to the current flowing through it. This is so the driver gets a visual indication when one of the turn signal bulbs burns out. (ISTR that was actually a US safety requirement.) Unfortunately, that also means it is sensitive to anything that reduces current through the bulb, like a high resistance connection somewhere or even having the bulb installed backwards. I believe it was JonMac who had a problem caused by corrosion inside the insulation of one of the wires!
However, I've also seen replacement flashers that were sold to fit earlier TRs but did not work properly. Bunch of years ago, I went through every model of 3 terminal flasher in stock at FLAPS, and none of them worked right, except for a Tridon EL13 (which is what I've been using ever since).