i've got a 1.9 skoda octavia (same engine as you) that used to have this
problem.
What's hapening is that the variable vanes in the turbo (these adjust how much exhaust the turbo gets) can get stuck with an accumulation of soot etc.
The computer sees this as over boost, decides there's a
problem and shuts off the turbo - so you feel it as a loss of acceleration.
A common history is of an engine that is nursed and not revved well regularly - this allows the soot to build up and not be burnt off.
I managed to eventually clear mine by regularly pushing the revs to 4000 (when the engine's warm). If the turbo cuts out you can reset it by turning off the ignition.
Over a couple of months mine slowly got better and it hasn't cut out in 6 months now.
If yours does not clear you'll either need the turbo fully stripped down and cleaned, or a new turbo
If you do a search on the mk1 forum here, or on the octavia section of
www.briskoda.com there are loads of threads about this