What's the difference between Camera.apk and com.sec.android.app.camera.apk?
The Serendipity ROM only contains Camera.apk and CameraFirmware.apk.  I would think that the version you're trying to copy over is being renamed by the system on reboot and the original Camera.apk is being restored.

What I would try:


Get the non-CWM version of the Camera.apk and put it on your SD card
On your phone, use Root Explorer or similar to mount /system/app/ as RW
Rename /system/app/Camera.apk to Camera.bak or something
Copy in the new apk from the SD card
Remount /system/app/ as RO, you may want to make sure /system/ is RO as well
Try to use the camera.  If it works, reboot and see if it still works.