Hi Tim,
a usual case why the Zaquencer might stop playing is that the clock has accidentally been set to “external” (=”etl”) on encoder 2 in the global menu. This way it waits for a start signal from an external midi host and won´t react to start/stop anymore. Simply enter Global menu and adjust encoder 2 to change to “int”.
Depending on whether you cleared the presets in the flash as well this setting might survive a reflashing of the original firmware and back to the Zaq.
When wanting to restore the Zaquencer to it´s defaults its important to do a re-init of the patterns/global parameters as well (hold “Page <” and “Start/Stop” before and during turning on the BCR). This will delete all musical patterns you might have created, so use only if you don´t have precious musical data stored on the device or have made a backup via SysEx.