help on electron detection

I'm working on a research topic that involves detection of secondary electrons induced by energetic ions. Secondary electron emission may
originate from the substrate from which ions emerge, or ions may be forced to pass through a thin carbon foil (thin enough not to generate too much straggling and cause loss of resolution) and secondary electrons are emitted from the foil.
The problem is the detection of electrons... The ions and electrons are separated by a crossed electric/magnetic filter: energetic ions travel straight to the ion detector and electrons are steered in the magnetic field onto the electron detector. The electron detector is a chevron microchannel plate (MCP). A time-of-flight spectrum is obtained when the signals from the two detectors are run in coincidence.
Although sounds rather straightforward, I've had difficulties for a long time with detection of electrons. I can get a reasonable electron count on the electron MCP; but when I run the two detectors in coincidence, I either get no spectrum, or a spectrum with spurious peaks. Most of time, the peaks do not make physical sense due to the geometry of the time-of-flight telescope.
If anyone has any past experience on this kind of a problem, I'd greatly appreciate comments.
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