I've done some further tests:
1) Whatever I do the emitter is pretty near ground (10s of mV away at a maximum, it never goes more than 60mV below ground at most negative "peak" value in any circuit setup (pulldown, cap in parallel...).
2) A close look at the base shows that the smaller the pulldown resistor the less delay between the falling edge of the signal from the NAND gate at the time when the base gets to ground, anything in the range of 180 ohms to 270ohms (40 to 120ns ) is very suitable to bring the base down fast enough for it to stay down a while before the NAND gate signal rises again.Tthere is no significant delay betwen the rise of the NAND gatevsignal and the rise of the base.
3) At a lower driving frequency the problem remains the same, without a pulldown the base never gets to ground, with it the delay between the NAND signalfalling and the base falling is the same for a given resistance as when driving at 3MHz.
4) I tried increasing and lowering the value of the 1K resistor, in all cases removing the pulldown stopped the base ever getting to ground, and with the pulldown the waveforms were fairly similar to with a 1K resistor between the NAND gate and the transistor's base.
I'm not keen on the capacitor in parallel to the 1K resistor because that causes some further ripples on the base signal which translate to extra ripples in the output, and a clean signal is quite important for my application. So as it seems to still work for a reasonably wide range of pulldown strengths, a range of series resistance values between the NAND' output and the transistor's base, and it still works if the transistor type is swapped... Is there anything wrong with the pulldown solution? Is it more vulnerable to suddenly not working in some circumstances than the capacitor solution would be, given it still worked with alteration of the values I would assume not?
P.S. baker clamp, that I tried earlier without success, although I haven't any Schottky's to hand right now (only normal small signal diodes), s had to use normal diodes. I'll remember to get some Schottky's for future uses when I next order any other components.
Thanks
EDIT: Just saw your latest reply. Using a 2N3904 instead of a BC337 gives similar results including a similar delaying the turning of of the base. I'll check through the datasheets of those transistors I have to hand right now and see which claim low capacitance.