Since you've got 2 sets of weights, this scenario could arise in 2 cases.
1. The machine learning algorithm you are using is an iterative or bayesian algo rather than a deterministic one.
2. You are using different sample of training data to train the weights.
In the first case, you anyways have a posterior distribution of weights so you can derive the final weights using any posterior point estimates.
In the second case, you basically want your model to 'generalize' well. so in this case you could use any cross validation or training/testing sample methods.
Instead of answering you question, I've suggested alternatives to what you're doing because, in general, there aren't any ways to compare similarity between weights. You basically try to get a distribution of weights and then choose your final point estimate.
Hope it helps.