with latest sdx and tclkit, I see the following:
$ sdx update -n efftcl.kit
EFFTCL: comparing with http://mini.net/sync.cgi ...
1 differences:
- <root>
$ sdx update efftcl.kit
EFFTCL: updating from http://mini.net/sync.cgi ...
1 changes applied.
$ $ sdx update -n efftcl.kit
EFFTCL: comparing with http://mini.net/sync.cgi ...
1 differences:
- <root>
$ mv efftcl.kit efftcl-prev.kit
$ sdx unwrap efftcl-prev.kit
170 updates applied
$ wget http://mini.net/sdarchive/efftcl.kit
$ sdx update -n efftcl.kit
EFFTCL: comparing with http://mini.net/sync.cgi ...
1 differences:
- <root>
$ sdx unwrap efftcl.kit
170 updates applied
# now, without making any changes:
$ sdx wrap efftcl.kit
170 updates applied
$ sdx update -n efftcl.kit
EFFTCL: comparing with http://mini.net/sync.cgi ...
Up to date.

It looks like this is due to an old tclkit which had flush problems - when
I upgraded my tclkit just now on macosx, which behaved exactly as you described,
the problem went away.
The sdx I tried was 2003/03/01 20:55:45 31803-15143, but the latest one has the
same effect, i.e. 2003/03/06 11:59:36 56635-48537.
The tclkit which failed had Mk4tcl 2.4.9.1, the latest is 2.4.9.2 works for me.
In a nutshell: latest revs sdx + tclkit should work fine for you.

$ sdx update -n /ldatae/bin/sdx.kit
SDX: comparing with http://mini.net/sync.cgi ...
Up to date.
$ sdx version /ldatae/bin/sdx.kit
2003/03/06 11:59:36 56635-48537 /ldatae/bin/sdx.kit
$ sdx version /ldatae/bin/tclkit.kit
2003/04/02 11:50:16 43115-49350 /ldatae/bin/tclkit.kit
$ sdx update -n /ldatae/bin/tclkit.kit
TCLKIT: comparing with http://mini.net/sync.cgi ...
Up to date.
$ sdx update -n /ldatae/bin/slidem.kit
SLIDEM: comparing with http://mini.net/sync.cgi ...
1 differences:
- <root>
$ sdx version /ldatae/bin/slidem.kit
2002/02/28 17:51:31 58325-59653 /ldatae/bin/slidem.kit
I continue to see this problem, with what sdx reports to be the latest
sdx and tclkit.

this has been traced to a starkit which does not yet use the latest header