I'm mastering a track. When I play it back through the effects I have loaded, it peaks at -0.5 dBFS. After I use the Apply Effects feature in the Process menu, it peaks at -1.3 dBFS. The effects I have loaded are not emulations of analog gear that might result in subtle differences with each pass. Every time I play it back through the effects, it's -0.5 and every time I apply the effects, it's -1.3. Can't figure out what's causing this. Any thoughts?

What FX?
 
Do you have a non-zero value for BounceBufSizeMsec= in AUD.INI? Some FX might render differently with different real-time vs. offline buffer sizes.
 
You might try a real-time (non-Fast) bounce to another track.
 

Equalizer and compressors react differently by "fast" bounce and real time. Some transients are sometimes treated differently.
I have a BounceBufSizeMsec = 300. Also the latency can have an effect to "real time".
 

Thanks for the responses. BounceBufSizeMsec is set to 0 in my AUD.INI file. I'll try bouncing in realtime to see if it makes a difference.