The fecal calprotectin (FCP) test is known to have false positives and false negatives within certain individuals, and thus for them the test is an unreliable indicator of gastero-intestinal tract inflammation. In that case, a C-Reactive Protein (CRP) blood test would be used instead as an indicator of inflammation levels (given that CRP is body-wide inflammation levels). I would propose that you fit into that outlyer group for whom the FCP test is just inaccurate. Scopes and biopsies don't lie, you've had multiple and no inflammation was shown.
Here's a couple articles on false positives and false negatives, and odds thereof.
clinchem.aaccjnls.org/content/49/6/861/www.ncbi.nlm.nih.gov/pubmed/12765980Abstract
BACKGROUND:
Fecal calprotectin (FC) has been proposed as a marker of inflammatory bowel disease (IBD), but few studies have evaluated its usefulness in patients with chronic diarrhea of various causes. We evaluated the diagnostic accuracy of a FC assay in identifying "organic" causes of chronic diarrhea in consecutive adults and children.
RESULTS:
In adult patients, FC showed 64% sensitivity and 80% specificity with 70% positive and 74% negative predictive values for organic causes. False-positive results (8 of 40 cases) were associated with the use of aspirin (3 cases) or nonsteroidal antiinflammatory drugs (1 case) and with the presence of concomitant liver cirrhosis (3 cases). False-negative results mainly included patients suffering from celiac disease (5 cases). Patients with IBD (9 cases) were identified with 100% sensitivity and 95% specificity. In pediatric patients, sensitivity was 70%, specificity was 93%, and positive and negative predictive values were 96% and 56%. False-negative results (11 of 35 cases) were associated mainly with celiac disease (6 cases) or intestinal giardiasis (2 cases).
CONCLUSIONS:
FC assay is an accurate marker of IBD in both children and adult patients. In adults, false negatives occur (e.g., in celiac disease) and false-positive results are seen in cirrhosis or users of nonsteroidal antiinflammatory drugs. Diagnostic accuracy is higher in children.