Are my loose stools being caused by gastroenteritis or prolonged antibiotic use?

[Slink2000]

I was recently traveling and have been taking 100mg of Doxycycline per day as an anti malarial drug.  First dose was taken on March 4th.

On March 17-18 I had an episode of travelers diarrhea (as did at least 50% of my fellow travelers, so it must have been something at the hotel breakfast or restaurant we ate at for lunch the day before).

Shortly thereafter, around March 29th, I came down with a common cold.  My poor body feels like a war zone!!!

As of today, my cold is clearing up, but I have been experiencing random episodes of heart burn, and serious abdominal cramping followed by really loose stools.  These movements are happening about twice a day.  I also find I have far more gas than usual.

I am currently taking a probiotic to try and restore some of the good flora in my intestinal tract.

My question is...do you think my gastroenteritis is being caused by the antibiotic use?  Or is it still just lingering from whatever I became infected with on my trip?  I do not want to stop taking the doxycycline as I want to ensure I am malaria free (I did get a few mosquito bites on my trip), but the thought of having heart-burn, gas, cramping, and really urgent, loose bowel movements for another three weeks is almost unbearable.

Do you have any thoughts?  Insight?  Suggestions?