Hello,
Please perform a test with a plugin provide by HikaShop ; like "paypal" for example.
I think that you won't be able to reproduce the issue and that the problem is coming from the JD Ideal payment plugin which do not do the order modifications as it should (aka it does not trigger the events for the plugins).
So, if the points are right deducted using an official HikaShop plugin ; you will have to contact the developer of JD Ideal plugin to get the fix for it.
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.