Вот типичные примеры сообщений об ошибках выдаваемых в случае несовпадения версий:

The subscription to publication 'SteelTracePub' could not be verified. Ensure that all Merge Agent command line parameters are specified correctly and that the subscription is correctly configured. If the Publisher no longer has information about this subscription, drop and recreate the subscription.  (Source: MSSQL_REPL, Error number: MSSQL_REPL-2147201019)
Get help: http://help/MSSQL_REPL-2147201019

или вот

The merge process could not connect to the message file from Subscriber '{7C68F2C1-475A-8A7D-B3A9-CD97CE7DCC55}:C:\Program Files\Intelmet\SteelTrace Server\WebServices\MobileReplication\30.37F18A17C1F2_33E54076-3538-3C74-947E-E9AE65FFEE34.IN'. Check to ensure that the server is running. (Source: MSSQL_REPL, Error number: MSSQL_REPL-2147198719)
Get help: http://help/MSSQL_REPL-2147198719

как видим ясности в диагностике ситуации они не прибавляют

Рекомендации очень простые. Всегда скачиваем необходимые последние версии этих продуктов с сайта Microsoft.

Microsoft SQL Server Compact 3.5 Service Pack 1 Server Tools
http://www.microsoft.com/downloads/en/details.aspx?FamilyID=fa751db3-7685-471b-ac31-f1b150422462

Microsoft SQL Server Compact 3.5 Service Pack 1 and Synchronization Services for ADO.NET version 1.0 Service Pack 1 for Windows Desktop
http://www.microsoft.com/downloads/en/details.aspx?FamilyID=dc614aee-7e1c-4881-9c32-3a6ce53384d9

The subscription to publication 'SteelTracePub' could not be verified. Ensure that all Merge Agent command line parameters are specified correctly and that the subscription is correctly configured. If the Publisher no longer has information about this subscription, drop and recreate the subscription. (Source: MSSQL_REPL, Error number: MSSQL_REPL-2147201019)
Get help: http://help/MSSQL_REPL-2147201019