The underlying problem here is that these apps are assuming, rightly so, that there will always only be one destination number (that is, only one SIM). Android doesn't officially support dual SIMs. From StackOverflow:
Android dual SIM card API
...the dual sim features are available but not documented and hence not officially supported. Having said that it doesn't mean that it will not be usable, it just means that android is not liable to support [that] functionality.
Dual SIM card Android
The current Android platform does not have support for multiple SIMs. A device with such support has been customized for this, so you will need to get information from that device's manufacturer for any facilities they have to interact with it.
A third question was even asked specifically about building an app for dual SIM handsets that has gone unanswered, likely for this reason. So, while it sounds like a reasonable expectation, without official support or APIs for developers to use I wouldn't expect many apps to account for two destination numbers.
From a consumer perspective this means that we're at the mercy of manufacturers to develop apps that function correctly with two SIM cards. Unfortunately it sounds like the your phone's stock messaging app isn't fitting this bill. Try reaching out to XOLO.