CVS-Directories disappear when uploading per SFTP-Client

[Dennis von Ferenczy]

I am running a cvs server "Concurrent Versions System (CVS) 1.12.9
(client/server)" on debian linux. 

When I do a checkout everything is fine and a "CVS" directory is present in
every directory of the checked out module. However as soon as I upload a
changed version of of my code using my SFTP-Client the CVS-Directory
disappears from the directory to which I have uploaded the file. As a result
of this CVS always thinks that the directory is not yet under CVS-control. 

that means when adding I get errors like 
"cvs add: in directory `.':
cvs [add aborted]: there is no version here; do `cvs checkout' first"

or when doing a "cvs update" in a directory with changed files I get errors
like: 
"cvs checkout: move away `project/history.txt'; it is in the way
C project/history.txt"

What could be causing this problem?

my .cvsrc File contains the following lines:
  cvs -q
  diff -u -b -B
  checkout
  update -d