If you installed crt emu in Windows in 15khz mode, I believe the default res (for the Windows desktop) is 480i. That kind of flicker is not unusual for 480i on some monitors.
There's s simple test to see if this is the problem. Run a 240p game in Groovymame like Street Fighter 2. If the issue goes away in 240p, there's nothing to be done (aside from changing monitors if having 480i is important).
Also, take a look at your settings in vm maker / arcade OSD. Did you select composite sync or did you leave it unchecked? It looks like your monitor connection is RGBHV, not RGBS. It's probably not this but it's worth looking just in case.