what version of FL are you using? what audio drivers are you using? (ASIO or DX), what audio interface are you using? are you running the extended memory version of FL or the regular one? what operating system and is it x86 (32bit) or x64 (64bit)... also, on the audio options for FL studio, what sample rate (44100 or 48000 Hz) and interpolation setting do you have?
There are some plugins that have issues with the FL wrapper default settings, try going to the wrapper setting (little gear icon on the top left), in the Processing tab check the 'process inactive inputs and outputs'... here some info from the FL studio help file:
Plugins behaving badly?
This section contains information to help bring wayward plugins back into line. Symptoms include issues like pops or crackling sounds but your underrun count isn't increasing (if it is click here). Plugins that play or render out of time with the timeline. CPU spikes, FL Studio lockups, crashes or rendering failures. There are three main places you can try making changes to settings and options to resolve issues with misbehaving plugins, they are:
Options and Settings
Open the Audio Settings and try the following:
CPU options - 'Multithreaded generator processing' (try off), 'Multithreaded mixer processing' (try off) & 'Align tick lengths' (try on/off).
NOTE: If the Audio settings 'Multithreaded processing' options appear to be the cause of problems, isolate the plugin/s that are behaving badly then permanently disable it for the plugin/s at fault. Do this by deselecting the Wrapper Additional Settings Menu 'Allow threaded processing' switch and saving the wrapper state. The options set will be remembered for that particular plugin next time it is opened, allowing you to turn the Audio settings multithreaded processing options back on (if desired).
Mixer options - 'Reset plugins on transport' (try turning off, if start/stop and moving around the Playlist is glitchy/slow).
ASIO4ALL - If you are using ASIO4ALL and getting crackling/glitches and the underrun count isn't increasing, check the Troubleshooting section of the ASIO4ALL settings.
The plugin wrapper 'Processing' tab. Try these settings to fix problems with spiking CPU load, crashes, no sound, rendering quality, loop-playback behavior and rendering sync (timing issues). Start with 'Use fixed size buffers' then try the other options if that is not successful.
The plugin wrapper 'Settings' tab. Try these settings to fix problems with MIDI, automation, GUI & patch-changing.
NOTE: It's also worth checking the FL Studio knowledge base section for more information as the data-base is updated with plugin specific information from time to time. Finally, if it's a 3rd party plugin and it's not working correctly in FL Studio, contact the developer, it's all care (that's why we offer so many options) and no responsibility here