We cannot reproduce the issue at the moment.
1.
Cache is stored in a local SQLite database. It is located in the user Application Data directory (C:\Users\{user name}\AppData\Roaming) by default and is named by the Salesforce.com or Database.com account name. Try removing these *.db files (they will be recreated on next conn.Open()). Does this help?
2. Download, set up, run
Fiddler and specify web requests sent when you updating MyCustomObject. For example, the requests in my case ("update dept set loc='12345' where dname='abcd'") are:
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[...]<s:Body xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><query xmlns="urn:partner.soap.sforce.com"><queryString>SELECT Id FROM Dept__c WHERE Dname__c = 'abcd'</queryString></query></s:Body></s:Envelope>
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[...]<s:Body xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><update xmlns="urn:partner.soap.sforce.com"><sObjects><type xmlns="urn:sobject.partner.soap.sforce.com">Dept__c</type><Id xmlns="urn:sobject.partner.soap.sforce.com">a0BA000000r0UihMAE</Id><Loc__c xmlns="">12345</Loc__c></sObjects></update></s:Body></s:Envelope>