I have done some more testing. I hacked the node example to add a third device in promiscuous mode to capture everything that goes on between the node and the Gateway. The output of this is included below. The first two numbers is the source and destination. After this comes the payload of the data captured, and whether an acknowledgement is requested or if the packet is an acknowledgement. It is clear from the trace below that the gateway actually sends the acknowledgement. So the problem is in the receiving end for the node.
Promiscuous at 868 Mhz...
SPI Flash Init OK ... UniqueID (MAC): D7 64 90 B4 C7 33 8B 2E
RFM69_ATC Enabled (Auto Transmission Control)
[2, 1] FLASH_MEM_ID:0xEF30 [RX_RSSI:-9] - ACK Requested
[1, 2] [RX_RSSI:-17] is ACK!
[2, 1] FLASH_MEM_ID:0xEF30 [RX_RSSI:-11] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-17] - ACK Requested
[2, 1] FLASH_MEM_ID:0xEF30 [RX_RSSI:-10] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-18] - ACK Requested
[2, 1] 1 [RX_RSSI:-9] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-18] - ACK Requested
[2, 1] 1 [RX_RSSI:-9] - ACK Requested
[1, 2] [RX_RSSI:-17] is ACK!
[2, 1] 1 [RX_RSSI:-10] - ACK Requested
[1, 2] [RX_RSSI:-18] is ACK!
[2, 1] 12 [RX_RSSI:-10] - ACK Requested
[1, 2] [RX_RSSI:-18] is ACK!
[2, 1] 12 [RX_RSSI:-10] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-17] - ACK Requested
[2, 1] 12 [RX_RSSI:-10] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-17] - ACK Requested
[2, 1] 123 [RX_RSSI:-10] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-17] - ACK Requested
[2, 1] 123 [RX_RSSI:-10] - ACK Requested
[1, 2] [RX_RSSI:-17] is ACK!
[2, 1] 123 [RX_RSSI:-10] - ACK Requested
[1, 2] [RX_RSSI:-18] is ACK!
[2, 1] 123 [RX_RSSI:-10] - ACK Requested
[1, 2] [RX_RSSI:-18] is ACK!
[2, 1] 123 [RX_RSSI:-11] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-17] - ACK Requested
[2, 1] 123 [RX_RSSI:-11] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-17] - ACK Requested
[2, 1] 123 A [RX_RSSI:-10] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-19] - ACK Requested
[2, 1] 123 A [RX_RSSI:-17] - ACK Requested
[1, 2] [RX_RSSI:-18] is ACK!
[2, 1] 123 A [RX_RSSI:-12] - ACK Requested
[1, 2] [RX_RSSI:-17] is ACK!
[2, 1] 123 AB [RX_RSSI:-12] - ACK Requested
[1, 2] [RX_RSSI:-17] is ACK!
[2, 1] 123 AB [RX_RSSI:-11] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-17] - ACK Requested
[2, 1] 123 AB [RX_RSSI:-11] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-18] - ACK Requested
[2, 1] 123 ABC [RX_RSSI:-11] - ACK Requested
[1, 2] ACK TEST [RX_RSSI:-18] - ACK Requested
[2, 1] 123 ABC [RX_RSSI:-11] - ACK Requested
[1, 2] [RX_RSSI:-17] is ACK!
Edit: I suddenly got it to work quite well by putting in 200 as the retry value for the node. Suddenly every packet started going through at the first try. However, this was not the case when switching gateway and node devices. Also, I was not able to reproduce this when switching the devices back again. I've done quite a little playing around with timing values as well, without success.