I found the answer to this question,
the first parameter of the method GetSiteProperties is the index from which site collection retrieval starts.
I tried the the following command
spp = tenant.GetSiteProperties(300, true);
which returned site collections from index 300.
So here is my code to get all site collections from sharepoint online
SPOSitePropertiesEnumerable spp = null;
var tenant = new Tenant(ctx);
int startIndex = 0;
while (spp == null || spp.Count > 0)
{
spp = tenant.GetSiteProperties(startIndex, true);
ctx.Load(spp);
ctx.ExecuteQuery();
foreach (SiteProperties sp in spp)
siteCols.Add(new SiteCol(sp.Title, sp.Url));
startIndex += spp.Count;
}
By the way, site collections are currently limited to 10000.