I have a dispute with a company refusing to pay an invoice.

I have done work for this company since 2012 and invoiced them after every job, after which they always promptly paid.
I advised of rates increases through email as well, never receiving reply but always paid without question.
In June 2013 I invoiced this company with a new rate and continued with jobs for them and invoicing until October, when I learned after checking payments I was not paid in full. I queried this and in November 2013 they said they would not pay the rate on my invoices.

I feel that they should have notified me that the new rate is not acceptable on receipt of my invoices, not letting me continue with work before the issue (that I was unaware of) was resolved.

I have subsequently taken the money off them and they are now threatening with legal action.

Do I have a foot stand on?

Are there options for independent freelancers to get help or advice in these situations?