The Unknown Command thing is due to having no return on the commands(Most, if not all callbacks with the Action: tag need a return of some sort), just add return Plugin_Handled; after the while loops.
Example:
PHP Code:
public Action:Command_One(client, args)
{
new entity = -1;
while ((entity = FindEntityByClassname(entity, "logic_branch"))!=INVALID_ENT_REFERENCE)
{
new String:entName[MAX_NAME_LENGTH];
GetEntPropString(entity, Prop_Data, "m_iName", entName, sizeof(entName));
if(StrEqual(entName, "bsm"))
{
SetVariantInt(1);
AcceptEntityInput(entity, "SetValueTest");
break;
}
}
return Plugin_Handled;
}
Running them multiple times shouldn't be a problem.