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Just thought I'd update this. It does not mean that I was paid more earlier on in the sick leave, it means that I had 5 days marked as sick, instead of 2 normal, contracted hours, 3 sick. This has lead to me accruing more sick days, and being penalised for it later on in the period, as I used up my contractual sick pay sooner.
I have found something on ACAS that supports my statement that it is punishing me for having a chronic illness and I should be paid properly for the hours I worked. This goes against my workplaces policy though.
However, it turns out that despite them employing over 7000 people, none of them have ever had a phased return to work, like I have. So they're investigating their policy. A bit of a relief, but any further advice would really be welcome!!