A huge study of Indonesian y-dna has come out last week, and it found 2 samples of R1b1(xR1b1b2) in Bali.
These samples could belong to the known haplogroups R1b1*, R1b1a, or R1b1b1.
A historic origin from Europe seems exceptionally unlikely.
A historic origin from India seems very unlikely. Indonesians do have quite a bit of y-dna of Indian origin, such as H, J, L, R2, and R1a, but India itself doens't seem to have any R1b1* or R1b1b1.
Also, the anomaly of these 2 West Eurasian lineages in Indonesia isn't the only one. The study found 3 samples of J*, a haplogroup so rare that in a study of 3,000 men, 700 of which belonged to J, there wasn't a single case of J*, every sample fell into J1 or J2. And yet, here we have in Indonesia 3 samples of J*, from Vietnam and Bali, out of just 18 total J samples. We might be looking at J3!
Very, very interesting results. Unfortunately, though the study did test for STRs, they didn't publish them.