Hello. alli does not affect the absorption of calcium - although it may somewhat affect the absorption of vitamin D since vitamin D is fat-soluble and needs fat to be abosrbed. As long as you are getting at least 800-1000iu of vitamin D a day, and eating normal diet, you should be fine. alli is not associated with causing any type of vitamin D deficiency.
Your sister is correct in recommending that you take your calcium in divided doses. You should take no more than 600mg per dose. A calcium supplement like Os-Cal should be taken with food - it is best absorbed when the acid in your stomach is at its highest - which is right after you eat. Do you take any other medications? Some medications, like Prilosec, Prevacid, Nexium, etc can prevent the body from absorbing all of the calcium from a supplement like Os-Cal. Let me know if this applies to you and I can help further.
Blood calcium levels are usually regulated by hormones - I am sure your doctor has tested you for other endocrine conditions that can affect blood calcium levels... like parathyroid issues?
Hope this helps! Best of health to you!
Maria Marzella Sulli, Pharm.D.