This sounds really difficult for all of you. You must be feeling like you're being pulled in 2 directions - wanting to keep your children happy but also wanting to keep the relationship with your partner.
Is there any chance their mother could be talking badly about the relationship/your partner? There is no doubt in my mind that my ex partner will do this to me and my bf as he won't like me being with someone else and won't want the children spending time around another man.
I'd keep things really light, spend time with them alone but also do fun things that include your gf too so it gives them a chance to see that whilst she's not their Mum, they are allowed to.enjoy her company and hopefully will gradually start to see her as a positive influence in their life. It will take time but try to be patient and try not to push anything on them.