Hi,
I'm unable to reproduce the issue you describe (I'm on SAP Basis 702, SP 11) and I'm trying to regularly implement OSS notes related to Smartform editor bugfixes. Could you tell please what is your SAP Basis release and support package? There are some quite recent bugfixes related to table/template painter, but none that fits the symptoms you describe.
Also, does the issue persist if you try to change the units from cm to, say, mm?
Could you please create a small test form with which you can reliably reproduce the issue in your system, export it as xml and attach it here?
Other than that, the text margins are best implemented using appropriate paragraph formats - not tiny-miny "dummy" table/template cells... 
cheers
Jānis