vandanagopal11,
Sorry that you are seeing this issue.
Please update to our latest release, MyEclipse 2013 SR1 and check whether you can replicate the issue ? Go to Help > Check for updates > Select ‘2013 SR1’ and click Apply.
If you can still replicate the issue in MyEclipse 2013 SR1, please answer some more queries to help us investigate further :
1) Can you please mention the exact steps in detail to help us reproduce this issue ? Also, please mention what type of application(Web/Maven/etc) you are deploying ?
2) Can you please mention the Tomcat server version in which you are deploying the application ? Also, please mention whether it is a local server ?
3) Can you please let us know whether the class timestamps are fine after the first deploy ?
Let us know how it works for you in MyEclipse 2013 SR1.