Yes they are normally very compatible. However, MSE v2 is picking up cfp.exe as a Trojan after Comodo Firewall auto-updates.
Description: This program has potentially unwanted behavior.
Recommended action: Review the alert details to see why the software was detected. If you do not like how the software operates or if you do not recognize and trust the publisher, consider blocking or removing the software.
Security Essentials detected programs that may compromise your privacy or damage your computer. You can still access the files that these programs use without removing them (not recommended). To access these files, select the Allow action and click Apply actions. If this option is not available, log on as administrator or ask the security administrator for help.
process:pid:2120 (which is cfp.exe)